In the 1920s 1. A. I. Oparin of Russia 2. John B.S Haldane of England Proposed a hypothesis on the probable origin of life. a. Atmosphere of early Earth must have contained methane (CH4), ammonia (NH4), Hydrogen (H2) and water vapor. b. Chemical reactions in said mixture of gases must have produced organic molecules and this could have given rise of the first living cells. 30 years layer 1. Harold C. Urey Proposed a model of the atmosphere of early Earth similar to Oparin and Haldane hypothesis on the probable origin of life. a. In 1952, he suggested an experiment to explore the origin of life under the conditions of his model of Earth’s primordial atmosphere. 1953 1. Stanley Lloyd Miller (American Chemist) Miller – Urey Experiment Theory of Chemical Evolution a. Source of Energy for the formation of the first organic molecules must have been gigantic fishes of lighting that must have constantly agitated the atmosphere of early earth. b. Source of energy must have been the abundant supply of ultraviolet radiation that could have reached Earth without an ozone shield to stop it. Theories and Hypothesis on how life started on Earth 1. Divine Creation – life forms may have been placed on Earth by supernatural or divine forces. The hypothesis that a divine God created life is at the core of most religion. 2. Extraterrestrial Origin – also referred as “panspermia”, proposes that meteors or cosmic dusts may have carried significant amounts of complex organic molecules to Earth, kicking off the evolution of life. It is hypothesized that an early source of carbonaceous material is extraterrestrial, although not proven yet. 3. Spontaneous origin – life evolved from inanimate matter as associations among molecules become more and more complex. As changes in molecules increased their stability initiate more and more complex associations, culminating in the evolution of cells. Many ideas have been developed based on the Spontaneous Origin a. At the ocean’s ridge – life may arise from the constantly forming bubbles at the edge of the ocean as suggested by some scientists. b. Deep in the earth’s crust – life may formed as by-product of volcanic activity where sulfuric minerals, iron and nickel recombine. Gunther Wachtershauser in 1988 and fellow scientist shows that these chemical combinations can form precursors of amino acid which can be later linked to peptides. c. Under frozen areas – just like Jupiter’s moon, Europa. It is hypothesized that life originated under a frozen ocean. d. Within clay – the silicate surface chemistry was hypothesized by some researchers emphasizing the positive charges of clay surface that may attract organic molecules and providing potential catalytic surface where life chemistry may have occurred. e. At the deep sea vent – another hypothesis that life originated at deep sea vents where the necessary prebiotic molecules are synthesized by metal sulfides in the vents. The positive charge of sulfides may have attracted the negative charge of biological molecules What is the age of the Earth – 4.6 billion years. What is the age of life on Earth – 3.5 billion years. Man could have first appeared about 100-150 thousand years ago as shown by artefactual evidences in various site. Periods under Paleozoic; Cambrian-Ordovician-Silurian-Devonian- What was earth like million years ago? Periods under the Mesozoic; Triassic-Jurassic-Cretaceous a. b. c. d. e. f. g. h. i. j. Earth is covered with thick blanket of ice. Lots of volcanoes and high mountains Large organism roamed the land The atmosphere did not have high oxygen content Asteroids/meteors frequently hit the surface. The lands moved a lot or the continents were a little closer to each other Volcanic eruptions A little bit warmer Plants were bigger Humans were not yet around Geologic Time Scale – is a tabular presentation of the history of life based on geologists’ study of rocks and the fossils they contain. All the pieces of information about earth are arranged chronologically from the oldest (at the bottom of the table) to the most recent (at the top of the table). Eon – the largest division of the geologic time scale, spans hundreds to thousands of years ago (mya). Era – division in an Era that span time period of tens to hundreds of millions of years. Period – a division of geologic history that spans no more than one hundred million years. Epoch – the smallest division of the geologic time scale characterized by distinctive organism. Geologic Time Record – a tabular representation of the major divisions of the earth’s history. The time intervals are divided and described from the longest to the shortest; Eons-Eras-Periods-Epochs. Each period has an approximated time frame and characterized by distinctive features (event and organisms) 4 eras – Precambrian-Paleozoic-Mesozoic-Cenozoic Carboniferous-Permian Period under Cenozoic; Tertiary-Quaternary The Geologic time is divided into: The four largest segments called Eons; Hadean-Archaean-Proterozoic- Phanerozoic The Phanerozoic is divided into eras; Paleozoic-Mesozoic-Cenozoic Extinction events and appearance of new life forms characterized by division among eras. Smaller division called periods characterized by a single type of rock system, make up each era. Some period are further divided into smaller time frame called epochs. Quaternary Tertiary Cretaceous Jurassic Triassic Permian Carboniferous Devonian Silurian Ordovician Cambrian Permian Devonian Ordovician-Cambrian Hadean Human evolution Mammals diversify Extinction of dinosaurs; first primates; first flowering plants First birds; dinosaurs diversify First mammals; dinosaurs Major extinction; reptiles diversify; pangea First reptiles; trees, seed ferns First amphibians; fish diversify First vascular plants Major diversification of animal life First fish; chordates (animal w/ backbone) Age of amphibians Age of fishes Age of Invertebrates Priscoan; atmosphere and ocean Charles Darwin – Western England, After graduation he joined the crew of the survey ship HMS Beagle as ship naturalist and conversation companion to Captain Robert Fitzroy. Voyage of the Beage – Dec. 1831; 22-year old, he left England as naturalist aboard the HMS Beagle for 5 year voyage around the world. Mission: Chart the South American Coastline - Freedom to explore on shore; Collected thousands of specimens of the exotic and diverse flora and fauna of South America; He noted that plants and animals of South America were very different from those of Europe; While on the beagle, he read the Lyell’s Principle of Geology During the 5-year voyage of the Beagle: Darwin’s observations challenged his belief that species do not change overtime. His observation of geological formation and species variation led him to propose by which species arise and change. – This process is known as Evolution. Aristotle (384-322 BCE) – arranged life forms on a scale on increasing complexity scala naturae – “scale of nature”. He observed that organisms vary in complexity and can be arranged based on their order of increasing complexity. He proposed that genetic change occurs in a species over time, which leads to their genetic and phylogenetic differences. The process is due to natural, not supernatural forces. Greek Philosopher – Father of Biology; Organized all things according to their Psyche [ a kind of soul]; Vegetative Psyche [lowest, you exist]; Animate Psyche [middle, you move]; Rational Psyche [Highest, you think]; Problems: Anthropocentric, Subjective, unable to prove existence of these psyches. EVOLUTION – as descent with modification. Proposing that Earth’s many species are descendants of ancestral species that were very different from those alive today. Can also be define as a change in the genetic composition of a population overtime. Is both pattern and a process Pattern of evolutionary change is revealed in observations about the natural world; Process of evolution consists of the mechanisms that have produced the diversity and unity of living things. Carolus Linnaeus: May 23, 1707- Swedish botanist, father of taxonomy. Widely known for two contributions – classification of binomial nomenclature of organisms. Classified nature into kingdoms, classes, orders, genera & species, which exist till today with some changes. Named 4,400 animal species & 7,700 plant species through his binomial nomenclature, a two-part scientific name in Latin for every species. He classified them in his book “Systema Naturae”. Was appointed Chief Royal Physician in 1747 & Knighted by King of Sweden in 1758. Binomial Nomenclature: Naming system that gives organisms a twopart scientific name – Genus species and classifying species into a hierarchy of increasingly complex categories. Dating Fossils – knowing the age of fossil can help a scientist establish its position in the geologic time scale and find its relationship with the other fossils. 2 ways to measure the age of a fossil a. Relative dating b. Absolute dating 1. Relative Dating – based upon the study of layer of rocks; does not tell the exact age; only compare fossil as older or younger, depends on their position in rock layer; fossil in the uppermost rock layer/strata are younger while those in the lowermost deposition are oldest. I. Law of Superposition – if a layer of rock is undisturbed, the fossil found on upper layers are younger than those found in lower layer of rocks. However, because the earth is active, rocks move and may disturb the layer making this; process not highly accurate; sedimental layer are deposited in a specific time – youngest rocks on top – oldest rocks at the bottom. II. III. Law of Original Horizontality – deposition of rocks happen horizontally-tilting, folding or breaking recently happened Law of Cross-Cutting Relationships – if an igneous intrusion or a fault cuts through existing rocks, the intrusion/fault is younger than the rock it cuts through. Index Fossils (guide fossils/indicator fossils/zone fossils): fossils from short-lived organism that lived in many places; used to define and identify geologic periods. Paleontology – the study of the remains of organisms of the past. Fossils – evidences of organism that lived in the past; they can be actual remains like bones, teeth, shells, leaves, seeds, spores or traces of past activities such as animal burrows, nests and dinosaur footprints or even the ripples created on a prehistoric shores. 2. Absolute Dating – determines the actual age of the fossil through radiometric dating, using the radioactive isotopes carbon-14 and potassium-40; considers the half-life or the time it takes for half of the atom of the radioactive element to decay; the decay products of radioactive isotopes are stable atoms. Radioactive Dating – dating organic matter up to around 70,000 years old. C-14 – it is based on the radioactive isotope of carbon; meaning its mass is 14 atomic mass units, or a.m.u. is produced in nature by cosmic ray bombardment of nitrogen atoms in the atmosphere. C-14 decays’ with a half-life, +40 years; examination of the amount of C-14, remaining today in a given organic material gives a fairly safe estimate of the age of said material. Radiocarbon dating has flaws; scientist discovered that the production of C-14 in nature is not exactly constant; thus some correction in the age of fossil remains had to be made. Types of Fossil Types of Fossil Description Examples Molds Impression made in a substrate = negative image of an organism. When a mold is filled Organic material is converted into stone Shells Casts Petrified Original remains Carbon film Trace/Ichnofossils Preserved wholly (frozen in ice, trapped in tar pits) Carbon impression in sedimentary rocks Record the movements and behaviors of the organism Per mineralization / The organic contents of bone and wood petrification are replaced with silica, calcite or silica pyrite, forming a rock-like fossils. Replacement Hard parts are dissolved and replaced by the other minerals like calcite, silica pyrite and iron. Carbonization or The other elements are removed and only coalification the carbon remained. Recrystallization Hard parts are converted to more stable minerals or small crystal turn into larger crystal. Authigenic Molds and casts are formed after most of preservation the organisms have been destroyed or dissolved. The theory that all organisms share a common ancestors is supported by many lines of evidences. Bones and teeth Petrified trees; coal balls (fossilized plants and their tissues, in round ball shape. Woolly mammoth; amber from Baltic sea region Leaf impression on the rock Trackways, toothmarks, glizzard rocks, corpolites (fossilized dungs), burrows and nests. - Fossils – are the remains and traces of past life or any other direct evidences of past life. Fossil Record – provides evidences that organisms have changed over time. - Ways of Fossilization Unaltered preservation Description Small organism or part trapped in amber, hardened plant sap. Fossil Record, Biogeographic Distribution, Anatomical Evidences, Biochemical Evidences, Evidence from Developmental Biology, Molecular Homologies. Artificial Selection - The remains of ancient life found in the oldest rocks are fewer and more primitive than those found in younger rocks. [Example: Earliest Fossils: Prokaryotes {blue-green bacteria}, 3.4-3.6 billion years ago. Findings: very simple forms of life lived in the past and over millions of year, probably gave rise to many kinds of organism with more complex body structures. The remains of many ancient plants and animals show structural similarities to certain organisms that lived today. Although none is exactly the same as the living species, also, - fossils found in younger rocks are not found much in older rocks. Findings: imply that ancestral forms gradually evolved over millions of years ang gave rise to offspring that are no longer exactly like themselves. In 2004, Paleontologist discovered fossilized remains of Tiktaalik roseae, nicknamed the “fishapod” because it is the transitional form between fish and four-legged animals, the tetrapods. Mix of fishlike tetrapod-like features. - Fossils such as Tiktaalik roseae provide evidences that the evolution of new groups involves the modification of preexisting features in older groups. The evolutionary transition from one form to another. Anatomical transitions during the evolution of whales. Transitional fossils, such as Ambulocetus and Basilosaurus, support the hypothesis that modern whales evolved from terrestrial ancestors that walked on four limbs. These fossils show a gradual reduction in the hand limb and a movement of the nasal opening from the tip of the nose of the head – both adaptations to living in water. Biogeography Each type of marsupial in Australia is adopted to a different way of life. All the marsupials in Australia presumably evolved from a common ancestors that entered Australia some 60 million years ago. Divergent Evolution = Adaptive Radiation Tortoises adapted to different habitats as they spread from the mainland to the different islands. Adapted to similar environments, independently from different ancestors. but evolved Sugar Glider In Australia is a marsupial more closely related to Kangaroos that North American Flying Squirrels Because its ancestors were marsupials. Convergent Evolution Whales and sharks have a similar body design even though they are very different organisms [one is a fish; the other, a mammal] because they have independently adapted to living in a similar environment. Biogeographical Evidence Biogeographical differences; provided evidence that variability in a single, ancestral population can lead to adaptation to different environments through the forces of natural selection. Competition for resources appears to provide some of the pressure that leads to diversification. Anatomical Evidence Similarities in Structure Homologous Structure Structures that are similar because of common ancestry | Organisms which undergo similar structures have close evolutionary ties. [Limbs of human-cat-whale-bat]. Forelimbs of all mammals share some arrangement of bones that can be traced to same embryological origin. Amnion – bag of waters; the extraembryonic membrane of birds, reptiles and mammals, which lines the chorion and contains the fetus and the amniotic fluid. Vestigial Organs – some homologous structures are vestigial and have no useful function even though they are still present. [Example: Hipbones and pelvis in whales and boa constrictors. Cecum {appendix} in human. Skink legs Embryology – development of vertebrate embryos follow the same path. [Fish-salamander-tortoise-chicken-rabbit-human]. Series of changes in body structure that an animal goes through from egg to adult. Same groups of undifferentiated cells developed in the same order to produce the same tissues and organs of all vertebrates, suggesting that they all evolved from a common ancestors. Why grow a tail and then lose it? Human embryo has a tail at 4 weeks which disappears at 8 weeks. Pharyngeal pouches become gills in fish, part of throat/ears in humans. Biochemical Evidences All living organisms use the same basic biochemical molecules, including DNA (deoxyribonucleic acid), RNA (ribonucleic acid) and ATP (adenosine triphosphate). Organism use a triplet nucleic-acid code in their DNA to encode for 1 of 20 amino acids that will form their proteins. The sequence of amino acids of some proteins is similar across the tree of life. The sequence of amino acids in the human version of cytochrome c, a protein essential to cellular respiration, is remarkably similar of that of yeast. Evidences from Developmental Biology Many developmental genes are shared among all animals ranging from worms to humans. It appears that life’s vast diversity has come about by a set of regulatory genes that control the activity of other genes involved in development. Hax, or homeobox, genes orchestrated the development of the body plan in all animals, from invertebrates (such as sea anemones and fruit flies) to humans. Function of Hax Gene A change in the timing and duration of the expressions of hax genes that control the number and type of vertebrae can produce the spinal column of a chicken or the longer spinal column of a snake. Molecular Homologies All life forms share same genetic machinery (DNA & RNA). Universal Genetic code. Important genes share highly conserved sequences. Similarities in DNA and protein sequences suggested relatedness. Similarities in karyotypes suggest an evolutionary relationship. Even differences show relatedness Chimpanzees have 2 smaller chromosomes pairs we don’t have Humans have 1 larger chromosome pair [#2] they don’t have. Protective chromosomes. telomere sequences found at ends of Telomeres in Middle Human chromosomes is only human chromosome that has telomere sequences at the ends but also in the middle… suggesting it was made by joining two other chromosomes together. Extra Centromere Chromosome #2 has a second inactive centromere region… suggesting it was made by joining two other chromosomes together. Allele Frequency – portion of specific allele in the population. The percentage of each allele in a population’s gene pool. Artificial Selection Gene Pool – the allele of all genes in all individuals in a population. Works nature provides the variation through mutation and sexual reproduction and humans select those traits that they find useful. [Ex. We have selected for and bred cows to produce more milk, turkeys with more breast milk ect.] Theodosius Dobzhansky, March 1973/ Geneticist, Columbia University 1900-1975 “Nothing in Biology makes sense except in the light of evolution”. Hardy-Weinberg Principle p2 + 2pq + q2 = 1 [can measure the genotype frequencies of a non-evolving population] The frequency of the D and d alleles in each gametes [sperm and egg] in this population would be the same as the allele frequencies, so that 20% of alleles in eggs and sperm will be D, and 80% of alleles in eggs and sperm will be d. Charles Darwin Theory of Evolution Darwin observed that populations, not individuals, evolve. But he could not explain how traits change overtime. Now we know that genes interact with the environment to determine traits – the diversity of individuals within that population. Because genes and traits are linked, evolution is really about genetic change – or more specifically, evolution is the change in allele frequencies in a population over time. Genes Population Evolution Microevolution – evolutionary change within populations. Populations – a group of organisms of a single species living together in the same geographic area. Compute the change in gene frequency from one generation to another generation. Allele – genes governing variation of the same character that occupy corresponding positions on homologous chromosomes. Change in p and q from generation 1 to 2: ∆𝑝 = 𝑝1 − 𝑝1 = 0.37 − 0.34 = 0.03: ∆𝑞 = 𝑞2 − 𝑞1 = 0.63 − 0.66 = −0.03 This means that there is increase in the frequency of p by 0.03 and a corresponding decrease in q after one generation of selection against the white phenotype. Hardy-Weinberg Equilibrium A population in which allele frequencies do not change over time. A stable, non-evolving state. The Hardy-Weinberg equilibrium is a constancy of gene-pool allele frequencies that remains stable from generation to generation if certain conditions are met. 1. No mutation: no new alleles can arise by mutation. 2. No migration: no new members [and their alleles] can join the population, and no existing members can leave the population. No gene-flow, random mating, no genetic drift, and no selection. When gene-pool frequencies change, microevolution occurs. Deviations from Hardy-Weinberg equilibrium allows us to detect microevolutionary shifts. Mutations occurs when the DNA sequence has changed. Which can serve as a source of new genetic variation. Migration Gene flow is the movement of alleles between populations. Occurs when plant and animals migrate, or more specifically their gametes move, between populations. When gene flows brings a new or rare allele into a population, the allele frequency in the next generation changes. Gene flow in plants may result when pollen from one plant fertilizes plant in another population. Small Population Size Genetic drift is when chance events cause allele frequencies to change. Both the bottleneck effect and founder effect result from the loss of genetic variation within the population. Genetic drift refers to changes in allele frequencies of a gene pool due to chance events. Such events remove individuals, and their genes, from a population at random – without regard for phenotype or genotype. Genetic drift occurs when, by chance, only certain members of a population, [green frogs] reproduce and pass on their alleles to the next generation. A natural disaster can cause the allele frequencies of the next generation’s gene pool to be different form those of the previous generation. Genetic drift can be a powerful force for evolutionary change, especially in small populations. The smaller the population, the more genetic drift impacts in the allele frequencies. A large population can suddenly become very small, A bottleneck effect is a type of genetic drift in which the loss pf genetic diversity is due to natural disasters [e.g. hurricane, earthquakes, or fire], disease, overhunting, overharvesting or habitat loss. A founder effect, another type of genetic drift, is similar to a bottleneck effect except that genetic variation is lost when a few individuals break away from a large population to found a new population. Consequences of bottleneck and founder effect. a. The gene pool of a large population contains four different alleles, represented by colored marbles in a bottle, each with a different frequency. b. A population bottleneck occurs. The marbles, or alleles, that exit the bottle must pass through the narrow neck into the cup. The new gene pool will have a fraction of the alleles from the original population. c. The gene pool of the new population has changed from the original. Some alleles are in high frequency, while some are not present. Nonrandom Mating Nonrandom mating alone does not cause allele frequencies to change. Nonrandom mating however, does affect how alleles in the gene pool assort into genotypes, thus affecting the phenotypes in a population. In a randomly mating population, the alleles in the gene pool assort at random. When mating is nonrandom, gametes, and thus alleles, assort according to mating behavior. Type of nonrandom mating, called assortative mating, occurs when individuals choose a mate with a preferred trait, such as a particular coat color, feather length or body size. Assortative mating brings together alleles for these traits more often than would happen by chance. Natural Selection A population in Hardy-Weinberg equilibrium has phenotypes that are equally likely to survive and reproduce. One genotype does not have an advantage over another. But in nature, some phenotypes do have a reproductive advantage. Individuals who have an advantageous phenotype often pass on the allele for this trait to their offspring. Over time, selection for this advantageous trait increases the frequency of the alleles associated with it, while other alleles decrease. Most of the traits of evolutionary significance are polygenic, controlled by many genes. Natural selection favors the most adaptive variant for a given environment. Three types of natural selections; 1. Stabilizing selection – the intermediate variation is the most adaptive, and is found in human birth weight. 2. Directional selection – either of the extreme phenotypes is favored, as when body size increases overtime 3. Disruptive selection – two or more extreme phenotypes are adaptive, the curve forms two peaks, as when british land snails have one of two different banding patterns of shell color. Sexual selection is about reproductive success, or fitness. Males produce many sperm and compete in inseminate females. Females produce few eggs and are selective about their mates. Traits that promote reproductive success, such as sexual dimorphism, are shaped by sexual selection. A cost benefit analysis helps a male determine if it is worth competing for mates. Dominance hierarchy provide dominant males greater reproductive opportunities than lower-ranking males. A territory is defended with specific behaviors known as territoriality. Biological differences between the sexes may promote certain mating behaviors because they increase fitness. Maintenance of Diversity Despite constant natural selection, genetic diversity is maintained. Mutations and recombination still occur, gene flow among small populations can introduce new alleles, and natural selection itself sometimes results in variation. In sexually reproducing diploid organisms, the heterozygote acts as a repository for recessive alleles whose frequency is low. In regard to sickle-cell disease, the heterozygote is more fit in areas where malaria occurs; this is known as the heterozygote advantage. a. Genes - The basic unit of heredity passed from parent to b. c. d. e. f. g. child. Genes are made up of sequences of DNA and are arranged, one after another, at specific locations on chromosomes in the nucleus of cells. Population - Population is a group of organisms of one species that interbreed and live in the same place at the same time. A group of individuals of the same species within a community. The nature of a population is determined by such factors as density, sex ratio, birth and death rates, emigration, and immigration. Allele Frequency - Allele frequency refers to how common an allele is in a population. It is determined by counting how many times the allele appears in the population then dividing by the total number of copies of the gene. [p + q = 1] Genotype Frequency - Genotype frequency in a population is the number of individuals with a given genotype divided by the total number of individuals in the population. In population genetics, the genotype frequency is the frequency or proportion (i.e., 0 < f < 1) of genotypes in a population. [𝑝2 + 2𝑝𝑞 + 𝑞2 ] Population Genetics - Population genetics is a field of biology that studies the genetic composition of biological populations, and the changes in genetic composition that result from the operation of various factors, including natural selection. Gene Pool - A gene pool refers to the combination of all the genes (including alleles) present in a reproducing population or species. A large gene pool has extensive genomic diversity and is better able to withstand environmental challenges. Gene Flow - Gene flow, the successful transfer of alleles from one population to another, is now known to vary considerably among species, populations, and individuals as well as over time. h. Genetic Drift - Genetic drift is the change in frequency of an existing gene variant in the population due to random chance. Genetic drift may cause gene variants to disappear completely and thereby reduce genetic variation. It could also cause initially rare alleles to become much more frequent, and even fixed. i. Mutation - A Mutation occurs when a DNA gene is damaged or changed in such a way as to alter the genetic message carried by that gene. A Mutagen is an agent of substance that can bring about a permanent alteration to the physical composition of a DNA gene such that the genetic message is changed. j. Bottleneck Effect - Population bottlenecks occur when a population's size is reduced for at least one generation. A population bottleneck or genetic bottleneck is a sharp reduction in the size of a population due to environmental events such as famines, earthquakes, floods, fires, disease, and droughts; or human activities such as specicide, widespread violence or intentional culling, and human population planning. k. Founder Effect - In population genetics, the founder effect is the loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population. It was first fully outlined by Ernst Mayr in 1942, using existing theoretical work by those such as Sewall Wright. Founder effect, as related to genetics, refers to the reduction in genomic variability that occurs when a small group of individuals becomes separated from a larger population. l. Nonrandom Mating - Nonrandom mating occurs when the probability that two individuals in a population will mate is not the same for all possible pairs of individuals. m. Assertive Mating - assortative mating, in human genetics, a form of nonrandom mating in which pair bonds are established on the basis of phenotype (observable characteristics). For example, a person may choose a mate according to religious, cultural, or ethnic preferences, professional interests, or physical traits. Systematics: [study of the kinds and diversity of organisms and of any and all relationships among them] Taxonomy Identification Description Nomenclature Classification of Organisms Goal of Systematics 1. Tracing phylogeny [the study of biological diversity in an evolutionary context] 2. Use data ranging from fossils to molecules and genes to infer evolutionary relationships. [information enable biologist to construct a comprehensive tree of life that will continue to be refined as additional data are collected] Taxonomy – theory and practice of classifying organisms. Modern Taxonomy – now based on evolutionary relationships. Taxonomical study: Structural similarities Chromosomal Structures [karyotypes] Reproductive potential Biochemical similarities Comparing DNA & Amino Acids Embryology/Development Breeding behavior Geographic distribution Classification – method of grouping organisms; arranging entities into some type of order to provide a system for sorting and expressing relationships between these entities. Nomenclature – formal naming of taxa according to some standardized system. For plants, fungi and algae, rules for naming are provided by the International Code of Botanical Nomenclature. For animals, rules on naming are based of the International Code of Zoological Nomenclature. Identification – is the process of associating an unknown taxon with a known one Description – is the assignment of features or attributes [characters] to a taxon. Hierarchy – a system of organizing groups into ranks according to status; putting groups at various levels according to importance Carolus Linnaeus [1707-1778] Swedish botanist and made the greatest contribution to taxonomy. He decided that organisms should be grouped based on similarities in body structure. Established binomial nomenclature: two part system to name and classify organisms. Kingdom Phylum Class Order Family Genus Species Hierarchical Classification - Taxonomic system named after Linnaeus. Linnaean System – places related genera in the same family, families into orders, orders into classes, classes into phyla [singular, phylum], phyla into kingdoms ad more recently kingdoms into domains. Species: Panthera pardus Genus: Panthera Family: Felidae Order: Carnivora Class: Mammalia Phylum: Chordata Domain: Bacteria; Kingdom: Animalia; Domain: Archaea Domain: Eukarya Taxon – named after taxonomic unit at any level of hierarchy. Andrea Cesalpino [1524-1603] – Italian physician. Published De plantis [1583]. He classified plants according to their fruits and seeds rather than alphabetically or by medicinal properties. He helped establish botany as an independent science and also made contributions to medical science and physiology. John Ray – in 1682, he had published a Methodus Plantarum Nova [revised in 1703 as the Methodus Plantarum Emendata]; his contribution to classification, which insisted on the taxonomic importance of the distinction between monocotyledons and dicotyledons, plants whose seeds germinate with one leaf and those with two, respectively; Ray’s enduring legacy to botany was the establishment of species as the ultimate unit of taxonomy; on the basis of the Methodus, he constructed his masterwork, the Historia Plantarum, three huge volumes that appeared between 1686 and 1704. Augustus Quirinus Rivinius [1652-1723] – his Introductio generalis in rem herbariam [Leipzig, 1690]; divided plants into eighteen classes, based on the regularity and number of petals and also on the fruit as whether the fruit was bare or surrounded by a dry or fleshy pericarp [the main part of the fruit excluding the seeds which develops from the wall of the ovary, Webb [2012]. Joseph Pitton de Tournefort – Elements de Botanique [1694]; placed primary emphasis on the classification of genera, basing his classification entirely upon the structure of the flower and fruit; he excelled in observation and description, and some of his generic descriptions are still acceptable; he was less innovative in theory, however, for he denied the sexuality of plants, and the classifications that he put forward above the level of the genus were often artificial. Phylogeny – a family tree for the evolutionary history of a species; the evolutionary history of a species or a group of species The root of the tree represents the ancestral lineage Tips of the branches represent descendents of the ancestor Movement upward shows forward motion through time Speciation – a split in the lineage. Shown as a branching of the tree. Robert Whittaker – American plant ecologist, active in 1950s to the 1970s; he was the first to propose the five kingdom taxonomic classification of the world’s biota into the Animalia, Plantae, Fungi, Protista and Monera in 1969. Carl Woese (Evolutionary Biologist) – microbiologist who revolutionized the field of phylogenic taxonomy; the tree of life originally included two domains, prokaryotic and eukaryotic, until Woese disproved this hypothesis through the use of ribosomal RNA [rRNA]; he sequenced and compared the 16S rRNA [a component of the small subunit of a prokaryotic ribosome] of bacteria and elucidated that Archaea had evolved separately from the universal ancestor of all life, simultaneously setting the standard for determining evolutionary relatedness among organisms; these studies allowed him to propose the idea that RNA was the precursor of life on Earth because of its catalytic tendencies, stability and ability to store genetic. Phylogenetic systematics [cladistics] – branch of the systematics concerned with the inferring phylogeny. Cladogram/Phylogenetic Tree – branching diagram that conceptually represents the best estimate of phylogeny. Polytomy – branch point from which more than two descendants groups emerge. Signifies that evolutionary relationship among the taxa are not yet clear. Taxa D-F A branching diagram to show the evolutionary history of a species; helps scientists understand how one lineage branched from another in the course of evolution. The connection between classification and phylogeny. Hierarchical classification can reflect the branching patterns of phylogenetic trees. Tree traces possible evolutionary relationship between some of the taxa within order Carnivora, itself a branch of class Mammalia. Branch point [3] represent the common ancestor of taxa A, B, and C; The position of branch point [4] to the right of branch [3] indicates that taxa B and C diverged after their shared lineage split from that of Taxon A; The taxa B and C are sister taxa, groups of organisms that share an immediate common ancestors [4] and others closest relatives. Rooted – which means that a branch point within the tree represent the most recent common ancestor of all taxa in the tree. Basal Taxon – refers to a lineage that diverges early in the history of a group and hence like taxon G lies on a branch that originates near the common ancestor of the group. The branch point [2] represent the most recent common ancestors of coyotes and gray wolves. Shared characters are used to contstruct phylogenetic trees. In reconstructing phylogenies: 1. Distinguish homologous features from analogous ones. 2. Choose a method of inferring phylogeny from these homologous characters. Cladistics – a system of classification based on phylogeny; derived characteristics/traits: appear in recent parts of a lineage but not in older members. Clades – are the lines of a cladogram; these represents sequences of ancestraldescendant populations through time, ultimately denoting a descent; includes an ancestral species and all the descendants; like a taxonomic ranks, are nested within the larger clades. 3. Polyphyletic ‘many tribes’ Includes taxa with different ancestor. Node – point of divergence of one clade into two different clades. Internode – region between two nodes. Taxon is equivalent of a clade only if it is: 1. Monophyletic ‘single tribe’ Signifies that it consists of an ancestral species and all of its descendants. Shared ancestral character – a character that originated in an ancestor of the taxon. Shared derived character – an evolutionary novelty unique to a clade. Unique to particular clades. Out group – a species or group of species from an evolutionary lineage In group – that is known to have diverged before the lineage that includes the species. 2. Paraphyletic ‘beside the tribe’ Consists of an ancestral species and some but not all of its descendants. The tree was constructed by comparing the sequences of homologs of the gene that play a role in development. Drosophila was used as an out group. The branch length are proportional to the amount of genetic change in each lineage; varying branch lengths indicate that the gene has evolved at different rates in different lineage. This tree is based on the same molecular data, but here the branch points are mapped to dates based on fossils evidence. Thus, the branch lengths are proportional to time. Each lineage has the same total length from the base of the tree to the branch tip, indicating that all the lineages have diverged from the common ancestor for equal amounts of time. Classification is linked to Phylogeny In certain similarities among organisms may lead taxonomist to place a species within a group of organisms [genus/family] other than the group to which it is closely related; If systematists conclude that such mistakes has occurred, the organisms may be reclassified [that is placed in a different genus/family] to accurately reflect its evolutionary history. Lines of evidence that to infer evolutionary relationships 1. Fossil Evidences 2. Homologies – similar characters due to relatedness [shared ancestry]; homologies can be revealed by comparing anatomies of different living things, looking at cellular similarities and differences, studying embryological development, and studying vestigial structures within individual organisms; organisms that are closely related to one another share many anatomical similarities. 3. Biogeography – the geographic distribution of species in time and space as influenced by many factors, including Continental Drift and log distance dispersal 4. Molecular clocks help track evolutionary time – the base sequences of some regions of DNA change at a rate consistent enough to allow dating of episodes in past evolution. Other genes change in a less predictable way. Molecular Clock – a yardstick for measuring absolute time of evolutionary change based on the observation that some genes and other regions of genomes appear to evolve at constant rates.