Life Origins Evolution Classification Edited by L Bridge

1. 1 Biology: The Study of Life (A review) • Biology: The study of living & once living (“paleobiology”) things • Scientists find it difficult to come up with one single definition for life, so we use a list of criteria. • Living things share the following characteristics in common (Is it alive? ): – – – – Made of cells Display organization Require input of energy and materials Reproduce Respond to stimuli Are homeostatic Grow and develop Adapt to their environment, evolve 28 -2

Evolution of Life 28 -3

Origin of Life • Age of Planet Earth - 4. 6 billion years • Oldest fossils - 3. 5 billion years – Australian microfossils – Marine – Resemble Archaebacteria 4

Chemical Evolution of Life – The common ancestor for all living things was the first cell or cells. – Under the conditions of the primitive Earth, it is a possibility that a chemical reaction produced the first organic compounds & then first cell(s). • Most Probable Formation of the First Cells: Step 1: Inorganic molecules reacted to form organic molecules Step 2: Organic molecules polymerized to become macromolecules Step 3: Plasma membrane formed Step 4: “Protocells” formed 28 -5

Oparin’s “Chemosynthesis” Hypothesis 1924 - Theorized that small organic molecules would have then given rise to larger organic molecules and finally macromolecules (Proteins, Carbohydrates, Fats, Nucleic Acids) Alexander Oparin What we know about the “young” planet earth: • Early atmosphere: methane, ammonia, hydrogen, carbon dioxide, & water vapor (no oxygen) • volatile, volcanic activity, electrical storms, lots of UV (no ozone) • To Oparin, this sounded like the “recipe” for a chemical reaction that would lead to formation of organic molecules (like amino acids) that would be the components of early cells! 6

Origin of the First Cell(s) Can we test/prove this? Yes, to a point 7

Origin of Life • Evolution of Small Organic Molecules – Early life may have arose in the primitive oceans, out of a “primordial soup” of organic molecules – Miller and Urey Experiment (1953) • Hypothesized that formation of small organic molecules is possible, from inorganic raw materials 8

The Result • At the end of one week of continuous operation Miller and Urey observed that as much as 10 -15% of the carbon within the system was now in the form of organic compounds. • Two percent of the carbon had formed amino acids • Sugars, lipids, and some of the building blocks for nucleic acids were also formed. • Nucleic acids (DNA, RNA) themselves were not formed. 9

Origin of Life • Evolution of Small Organic Molecules – Some scientists hypothesize life began in hydrothermal vents deep in the ocean 10

“Panspermia” • An alternate theory is that the earliest organic molecules may have arrived on our young planet in meteorites • These molecules reacted and condensed into the earliest cells Evidence of organic compounds HAS been found in recovered meteorites. The Murchison and Murray meteorites are some of the best-studied examples. http: //science. nasa. gov/ headlines/y 2001/ast 20 d ec_1. htm 11

More evidence on the origin of the first cells (“protocells”): – Under specific conditions of p. H, ionic composition, and temperature concentrated mixtures of macromolecules form coacervates – These are cell-like droplets formed from dissimilar substances; linked a. a. and sugars – Coacervate droplets absorb and incorporate many substances – May form a semi permeable boundary around droplet – In lipid environment, phospholipids are known to automatically form liposomes-may be the way plasma membranes first formed 12

Sidney Fox (1957) created membrane-bound “microspheres” in the laboratory • Although roughly cellular in appearance, microspheres in and of themselves are not alive. • Although they do reproduce asexually by budding, they do not pass on any type of genetic material. • However they may have been important in the development of life, providing a membrane-enclosed volume which is similar to that of a cell. • Microspheres, like cells, can grow and contain a double membrane which undergoes diffusion of materials and osmosis. 13

Origin of Life • The “True Cell” – …Is a membrane-bounded structure that can produce proteins (enzymes) that allow DNA replication • DNA RNA Protein – “RNA-first” hypothesis suggests that RNA developed before DNA, so first true cell would have had RNA genes • Some viruses have RNA genes • Reverse transcriptase produces DNA from RNA • RNA can act as both a carrier of information and as an enzyme (“ribozyme”) • Thomas Cech 14

27. 1 Origin of Life • The True Cell – other hypotheses: – “Protein-first” hypothesis suggest proteins evolved first • Complex enzymatic processes may have been necessary formation of DNA and RNA • Enzymes may have been needed to produce nucleotides and nucleic acids – The Cairnes-Smith hypothesis suggests RNA and protein evolved at the same time • RNA genes could replicate because proteins were already present to catalyze the reactions • But this supposes that two unlikely spontaneous processes would occur at once- formation of RNA and formation of protein 15

Origin of Life • The True Cell – Once protocells had genes, they could selfreplicate, they became capable of reproducing, and biological evolution began. 16

Origin of Life • The Heterotroph Hypothesis – Nutrition was plentiful in the ocean: “primordial soup” – Protocells were most likely heterotrophs • Implies that heterotrophs preceded autotrophs – Protocells probably used preformed ATP at first • Natural selection favored those that could extract ATP from carbohydrates • Fermentative process because oxygen was not available 17

The probable sequence of events: 1 st Heterotrophic prokaryotes: unicellular, simple, anaerobic, heterotrophic 2 nd Chemotrophic autotrophs: “Chemosynthesis”: carbon dioxide serves as carbon source for creating organic molecules, like methane; energy derived from chemical reactions Archaebacteria similar to 1 st autotrophs because make glucose by chemosynthesis rather than by photosynthesis 3 rd Photosynthetic autotrophs: brought about changes on earth. . . helped to add oxygen to the air. . . Cyanobacteria. . . atmosphere forming, cloud cover, ozone (protection) 4 th Cells become aerobic Important initial function of aerobic respiration may have been to bind oxygen & prevent damage to early organisms 18

• Prokaryotes arose about 3. 5 billion years ago • Eukaryotes came about 2. 1 billion years ago • Multicellularity came much later at 700 million years ago – First Eukaryotes: unicellular; membrane bound nucleus & organelles Most evolutionary events occurred in less than 20% of the history of life! 19

How cells are organized What are the two major types of cells in all living organisms? - Prokaryotic cells Thought to be the first cells to evolve Lack a nucleus Represented by bacteria and archaea - Eukaryotic cells Have a nucleus that houses DNA Many membrane-bound organelles All plant and animal cells are eukaryotic 28 -20

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The “Endosymbiont Hypothesis” Endosymbiosis: • Eukaryotic cells may have evolved from large prokaryotic cells invaded by small prokaryotic cells • Smaller, embedded cells may be ancestors of organelles; mitochondria/chloroplasts • Supporting evidence – Both mitochondria & chloroplasts contain own genes, different from rest of cell – Replicate independently from replication cycle of cell – Found in circular piece of DNA; prokaryotic arrangement 22

The Concept of Evolution • In biology evolution is simply defined as biological changes that have occurred in living organisms since the beginning of life. • Evolution is “descent with modification”, which is possible because of the changeability/malleability of the DNA code. – “Modifications” = random mutations can constantly change genotypes/phenotypes from generation to generation = novel variations of traits in the population • Evolution assumes a certain relatedness (“common ancestry”) between organisms. Evolution “for dummies 9: 58 http: //www. youtube. com/watch? v=Se. Tssvexa 9 s 23

Evolution is the Unifying Principle of Biology Evolution accounts for life’s unity and diversity • The history of life – Is a saga of a changing Earth billions of years old

• The evolutionary view of life – Came into sharp focus in 1859 when Charles Darwin published On the Origin of Species by Natural Selection Figure 1. 18

Darwin based his idea on the understanding of human-influenced selective breeding of domestic animals

Darwin’s basic suppositions in “On the Origin of Species…” • Variation (due to? ) • Competition (for? ) • Natural selection (the environment decides…) – “the cruelty of nature” – “the struggle for existence” – differential reproduction – “survival of the fittest” (Herbert Spencer) Figure 1. 19

Natural Selection • Darwin proposed natural selection as the mechanism for evolutionary adaptation of populations to their environments Population of organisms Hereditary variations Define “adaptation”? Figure 1. 20 Overproduction and struggle for existence Differences in reproductive success Evolution of adaptations in the population

• Natural selection is the evolutionary process that occurs when a population’s heritable variations are exposed to environmental factors that favor the reproductive success of some individuals over others 1 Populations with varied inherited traits 2 Elimination of individuals with certain traits. 3 Reproduction of survivors. Figure 1. 21 4 Increasing frequency of traits that enhance survival and reproductive success.

• Each species is one “twig” of a branching tree of life (phylogeny) – Extending back in time through ancestral species more and more remote • All of life – Is connected through its long evolutionary history

A Case Study in Natural Selection: Mimicry • In mimicry – A harmless species resembles a harmful species Flower fly (non-stinging) Honeybee (stinging) Figure 1. 26

Evolutionary Divergence http: //whyevolutionistrue. wordpress. com/2012/07/24/a-new-study-ofpolar-bears-underlines-the-dangers-of-reconstructing-evolution-frommitochondrial-dna/

• Darwin proposed that natural selection – Could enable an ancestral species to “split” into two or more descendant species, resulting in a “tree of life” Large ground finch Large cactus ground finch Small ground finch Large tree finch Geospiza Camarhynchus Green Gray Geospiza magnirostris psitacula Medium warbler Sharp-beaked fuliginosa Woodpecker Geospiza Medium finch tree finch ground conirostris finch Certhidea Geospiza. Cactus Cactospiza Camarhynchus olivacea fusca difficilis ground finch pauper pallida Geospiza Mangrove Small tree finch fortis Geospiza Camarhynchus Cactospiza scandens parvulus heliobates Vegetarian Cactus flower Seed eater finch eater Platyspiza crassirostris Insect eaters Ground finches Tree finches Bud eater Warbler finches Ex: Allopatric speciation Figure 1. 23 Common ancestor from South American mainland

Unity in the Diversity of Life • As diverse as life is – There is also evidence of remarkable unity 15 µm 1. 0 µm Cilia of Paramecium. The cilia of Paramecium propel the cell through pond water. 5 µm Figure 1. 16 Cross section of cilium, as viewed with an electron microscope Cilia of windpipe cells. The cells that line the human windpipe are equipped with cilia that help keep the lungs clean by moving a film of debris-trapping mucus upward.

Drawing evolutionary trees The phenetic approach is popular with molecular evolutionists because it relies heavily on character data - such as sequences - and requires relatively few assumptions. In this approach, a tree is constructed by considering the phenotypic similarities of the species without trying to understand the evolutionary history that brought the species to their current phenotypes. Evolutionary trees (Berkeley) Cladistics bases classification of a group of species solely on their most recent common ancestor. Cladistics uses shared derived characters. Animation “How to build a cladogram” You. Tube lesson on how to make a cladogram (10 min) Practice worksheet

• Concept 1. 3: Biologists explore life across its great diversity of species • Diversity is a hallmark of life Figure 1. 13

Classification of Living Things • Over a million species named (so far) • More identified every day • 2 -20 Million left to find? • Why? Need to organize information • Taxonomy = science of identifying and classifying organisms 37

Classifying life • Taxonomy – Is the branch of biology that names and classifies species according to a system of broader and broader groups Species Genus Family Order Class Phylum Ursus americanus (American black bear) Ursus Ursidae Carnivora Mammalia Chordata Animalia Figure 1. 14 Eukarya Kingdom Domain

The Three Domains of Life – Distinguished based on biochemical evidence (differences in r. RNA, genes) – Domains Archaea and Bacteria are unicellular organisms lacking membrane-bound organelles like nuclei (Prokaryotes) – Domain Eukarya is organisms whose cells have nuclei (Plants, Animals, Fungi and Protists)

Classification of Living Things • 3 Domains • Kingdom • Phylum (Division for plants) • Class • Order • Family • Genus • Species 40

Domain Archae • Prokaryotes – Single celled – Complex metabolic ability • Kingdom Archaebacteria – Found in extreme environments – Environments similar to those of early earth – First organisms similar to Archaea? 41

Domain Bacteria • Kingdom Eubacteria – Found almost everywhere – More of them than any other living thing – Some are parasites, causing diseases – Most are harmless and many are vital to human well being • Decompose our wastes • Make vitamins in our guts • Producing certain products that we use (yogurt, cheese) 42

Domain Eukarya – Protista- one celled organisms- producers or consumers (or both) – Fungi- molds, mushrooms; mostly decomposers – Plantae- multicellular plants; mostly producers – Animalia - multicellular animals from sponges to humans; consumers 43

Classification of Living Things • Within Kingdoms, organisms are sorted into Phylum, Class etc. • At species level organisms so closely related they can interbreed • Scientific name = Genus and species names (binomial nomenclature ex. Felis catus, Drosophila melanogaster, Homo sapiens • Genus includes other similar species ex. F. leo and F. tigris or Quercus rubra, Quercus alba • Genus ALWAYS starts with cap, species lower case • Genus and species names are always either underlined or italicized 44

Example: How are humans related to other animals? Domain Kingdom Phylum Class Order Family Genus Species Human Eukarya Animalia Chordata Mammalia Primates Hominidae Homo sapiens House cat Eukarya Animalia Chordata Mammalia Carnivora Felidae Felis catus 45

Evidence for Evolution 46

Phylogeny: the study of the evolutionary history of groups of organisms Plant evolution (cladogram) Like a “family tree” 47

Primates 48

Fossils as Evidence of Evolution – Hard body parts are preserved in most cases trilobite – Often embedded in sedimentary rock – Deposited in layers called strata • Each stratum is older than the one above and younger than the one below – “Transitional fossils” • Especially significant finds; represent evolutionary links between groups However fossilization is a relatively uncommon occurrence, usually requiring hard body parts and death near a site where sediments are being deposited, the fossil record only provides sparse and intermittent information about the evolution of life. 49

Transitional Fossils example: Archaeopteryx 50

Vertebrate groups 51

New Fossils Of Extremely Primitive 4 -Legged Creatures Close The Gap Between Fish And Land Animals Science. Daily (June 27, 2008) — New exquisitely preserved fossils from Latvia cast light on a key event in our own evolutionary history, when our ancestors left the water and ventured onto land. Swedish researcher Per Ahlberg from Uppsala University and colleagues have reconstructed parts of the animal and explain the transformation in the new issue of Nature. Tiktaalik 52

Geological Evidence of Evolution • Geological Timescale – History of Earth is divided into eras, then periods, and then epochs – Based on dating of fossil evidence – Relative dating method – determines the relative order of fossils because the fossil-containing sedimentary rocks occur in layers. Top layers are younger and thus the fossils in them are younger. Thus it is a matter of “What came first, second, third” – Absolute dating method - radioactive carbon dating (radiometric dating): Makes use of radioactive elements that decay into other more stable elements according to a strict timetable. 53

Radioisotope Dating • Ex: Radioactive 14 C (In Organic Matter) changes into 14 N (1/2 of 14 C will change into 14 N in 5, 730 yrs) • Assuming that organic matter always begins with the same amount of 14 C. • Goal is to compare the 14 C radioactivity of the fossil to that of a modern sample of organic matter. The amount of radiation left in the fossil can be converted to the age of the fossil. • Other similar methods are used to date rocks that are thought to be billions of years old. ex: Starting with 8 g of 14 C, down to 1 g; how much time has elapsed? ans: 8 4 2 1 = 5730 + 5730 = 17, 190 yrs 27 -54

Commonly used radioisotopes for dating: Parent Daughter Change in… Carbon-14 Nitrogen-14 5730 years Uranium-235 Lead-206 4, 470 million yrs Potassium-40 Argon-40 1, 208 million yrs Thorium-232 Lead-208 14, 010 million yrs Rubidium-87 Strontium-87 48, 800 million yrs 55

Geological/Fossil Evidence of Evolution • Background extinctions • “Mass Extinctions” – Large numbers of species become extinct in a short period of time • Remaining species may spread out and fill habitats left vacant – Five Major Extinctions have occurred – It is proposed that many mass extinctions have resulted from extraterrestrial events, volcanism, atmospheric fluctuations, global warming, cooling (ice ages), sea levels, etc. • However, a current SIXTH one is in progress due to human encroachment 56

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The last major mass extinction • The K-T Event – 65 million yrs ago – Killed off the dinosaurs, among others – Marked the end of the Cretaceous period, beginning of Tertiary • Clay from that period is high in iridium, an element in meteorites • Proposed that meteorites hit Earth and dust filled the atmosphere – Blocked sunlight, plants died – One reason why we don’t see some of the evolutionary ancestors today is because of mass extinctions. 58

Biogeographical Evidence of Evolution Biogeography is the study of the geographic distribution of species throughout the world – The Earth has six biogeographical regions • Each has its own distinctive mix of species – Barriers prevented evolving species from migrating to other regions – Continental Drift • The positions of continents and oceans has shifted through time • The distribution of fossils and existing species allows us to determine approximate timeline • Example: oldest camel fossils 45 -40 mya in N. America! 59

Continental Drift 60

Distribution of Large Cats 61

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Evidence of Evolution: Anatomical Evidence • Common descent offers explanation for anatomical similarities • Homologous Structures – Same underlying structure, adapted for different functions, same embryologic origin – Likely inherited from a common ancestor • Ex: human arm and whale forelimb 63

Analogous Structures Same basic function but different hereditary origins. Underlying anatomy is different, thus unlikely to have evolved from common ancestor ex: wing of bird and wing of an insect Not a good indicator of relatedness. More likely due to convergence. 64

Anatomical Evidence: Vestigial Structures Anatomical structures fully functional in one group and reduced, nonfunctional in another Ex: Modern whales have a pelvic girdle and hind leg bones 65

Probable origin of appendix Gastric caecum in herbivores 66

Evidence of evolution : Embryological Development 67

Biochemical Evidence of Evolution – All organisms use same basic biochemical molecules • DNA coding: A, T, C, G • Amino acid sequence of proteins – Many developmental genes are shared (homeotic) – Degree of similarity between DNA base sequences (and amino acid sequences of similar protein) indicates the degree of relatedness 68

Compare a homologous (shared) gene sequence. This can be used to quantify similarities/differences. • • • Canis lupus familiaris Canis lupus dingo Vulpes vulpes Canis rufus Provides verifiable data. 69

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…Or can use a shared protein sequence for comparison Muscle myosin sequence 71

The Molecular Clock • Based on the molecular clock hypothesis (MCH), this relates the amount of time since two species diverged to the number of molecular differences measured between the species' DNA or protein sequences or proteins. • It is sometimes called a “gene clock” or “evolutionary clock”. 72

The Molecular Clock 73

Significance of Biochemical Differences 74