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Biology
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BIOL 103
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Prof.
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Winter

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Biology 103 - Boag Section Table of Contents Chapter 14: Eukaryotic Chromosomes, Mitosis, and Meiosis (Review) Chapter 15: Inheritance and Phenotype Determination (Review) Chapter 18: Genetic Technology (Review) Chapter 20: Origin and History of Life Chapter 21: An Introduction to Evolution Chapter 22: Population Genetics Chapter 23: Origin of Species and Macroevolution Chapter 24: Taxonomy and Systematics Chapter 49: Animal Reproduction Chapter 52: An Introduction to Ecology and Biomes Chapter 53: Behavioural Ecology Chapter 54: Population Ecology Chapter 55: Species Interactions Chapter 56: Community Ecology Chapter 57: Ecosystems Ecology (Finish) Chapter 58: Conservation Biology and Biodiversity (Finish) Chapter 14: Eukaryotic Chromosomes, Mitosis, and Meiosis (14.3,14.4) Also known as "Materials and Processes for Procreation at the Cellular Level" Walter Sutton  The discovery that chromosomes come in pairs and that they carry genes - the unit of inheritance in 1903  This was made when he was an undergraduate student at Kansas University Eukaryotic Chromosomes  Nucleosome: Packaging of DNA with 8 histone proteins + 146 nucleotide base pairs. Creates a three- dimensional zigzag model Cell Division in Prokaryotes  Prokaryotes simple fission produces identical daughter cells... "asexual reproduction"  No mitotic spindle  Circular DNA molecules separate as the cell wall forms Cell Division in Eukaryotes  Eukaryotes use mitosis to produce identical daughter cells by means of asexual reproduction  Complex process involving cytoskeletal systems  Linear DNA strands separated by complex motor systems  Cytokinesis = splitting of cytoplasm Karyotyping (seeing if something is missing)  Step 1: A sample of blood is collected and treated with drugs that stimulate cell division. The sample is then subjected to centrifugation  Step 2: The supernatant is discarded and the cell pellet is suspended in a hypotonic solution. This causes the cells to swell.  Step 3: The sample is subjected to centrifugation a second time to concentrate the cells. The cells are suspended in a fixative, stained, and placed on a slide.  Step 4: The slide is viewed by a light microscope equipped with a camera: the sample is seen on a computer screen. The chromosomes can be photographed and arranged electronically on the screen. Human chromosomes  Somatic (body cells) have 2 sets of chromosomes (homologous chromosomes) and diploid chromosome: 46 in humans  Sex cells/Gamete: 1 set of chromosomes. haploid number of chromosomes: 23 in humans  Homologous chromosomes each existing as a pair of sister chromatids  Each chromosomes replicates prior to mitosis  At the start of mitosis, the chromosomes become compact  Kinetochore proteins attach centromere (a region of DNA beneath kinetochore proteins) to pieces of the chromosome to form a pair of sister chromatids. Eukaryotic cell cycle  Mitosis: Early Stages  Interphase: Chromosomes have already replicated during interphase  Prophase: Sister chromatids condense and spindle starts to form. Nuclear member begins to dissociate into vesicles  Prometaphase: Nuclear membrane has completely dissociated into vesicles and the spindle is fully formed. Sister chromatids attach to spindle via kinetochore microtubules.  Mitosis: Formation of Daughter Cells  Metaphase: Sister chromatids align along the metaphase plate (midplane). Microtubule organizing center helps to attach kinetochore microtubules to the kinetochore. (**Centrioles are not found in plants)  Anaphase: Sister chromatids separate and individual chromosomes move toward poles as kinetochore microtubules shorten. Polar microtubules lengthen and push poles apart  Telophase & Cytokinesis: Chromosomes decondense and nuclear membranes reform. Cleavage furrow separates the 2 cells. Animal Cell Cytokinesis  Actin and myosin-dependent proteins (like muscle proteins) help to form cleavage  Actin/myosin fibers pull like purse-sting, nip cells apart Daughter Cell Production in Plants  The mitotic spindle, no centrioles  Vesicles form out of the Golgi over the equatorial plate  They for a large vesicle and produce the new cell walls  pH affects turgidity of plants Regulating Cell Division (2 gene products)  Anaphase promoting complex: end of mitosis regulator. Kineases puts phosphorus/phosphates on a compound to regulate the cycle  Maturation promotion factor: begins mitosis (beginning regulator) Sex and Division  Sexual eukaryotes combine their DNA to produce progeny  Prepare DNA for combination with the DNA of another individual  Meioses - this DNA preparation process Sex and Diploidy (2N)  Gametes = Sex cells; gave 1 set of chromosomes, are thus 1n or haploid  Combine in new cell (the zygote) - beginning of a new individual  One from mother, one from father = 2N or diploid  There are two homologous chromosomes of each chromosomes type in a 2N organism  Mixes genes with parents = increase adaptability and variation compared to asexual reproduction Sex Provides Greater Variability  Increases ability to adapt to the environment  2N organisms more than just separate their homologous chromosomes during preparation of the sex cells  The homologous chromosomes come together : synapse  They forma synaptonemal complex, in which there is breakage and crossover of genetic material between chromatids of the two homologous chromosomes  Resulting homologous chromosomes, not the same as the parental homologous chromosomes; they have a mixture of genes  Produce a sex cell that is somewhat different in genetic complement from either parent  So when two gametes join during fertilization = resulting zygote has a different genetic complement from either parents  Sexual reproduction - mutations are diving forces for evolution Cladograms  Describes relatedness between animals/organisms First Meiotic Division (After Pre-meiotic interphase)  Homologous chromosomes synapse to form bivalents, and crossing over occurs. Chromosomes condense and the nuclear membrane begins to vesiculate  The Synaptonemal Complex:  DNA is precisely cut and recombined  The synaptonemal complex holds the chromatids of the homologous chromosomes close together until crossover is completed  "Perfect register" = if crossover occurs, identical DNA transcription will occur.  Crossover & Chiasmata (most important part of meiosis)  The region of crossover forms an X-shaped structure  This X-shape is called a chiasma (from the Greek) - chiasmata plural  Bivalents form, Crossing over occurs, Chiasma becomes visible as homologous chromosomes loose the synaptonemal complex.  Step 1: Prometaphase 1: Nuclear membrane completely vesiculates and bivalents become attached to kinetochore microtubules  Step 2: Metaphase 1: Bivalents align along the metaphase plate  Step 3: Anaphase 1: Homologous chromosomes separate and move toward opposite poles  Step 4: Telophase 1 and cytokinesis: Nuclear membranes re-form and the chromosomes decondense. The 2 cells are separated by a cleavage furrow. Note how the chromosomes have not split into sister chromatids, like in mitosis. Second Meiotic Division (Proceeds exactly as if it was mitosis)  Step 1: Prophase II: Sister chromatids condense and the spindle starts to form. Nuclear membrane begins to vesiculate  Step 2: Prometaphase II: Nuclear membrane completely vesiculates. Sister chromatids attach to spindle via kinetochore microtubules.  Step 3: Metaphase II: Sister chromatids align along the metaphase plate  Step 4: Anaphase II: Sister chromatids separate and individual chromosomes move toward poles as kinetochore microtubules shorten. Polar microtubules lengthen and push poles apart  Step 5: Telophase II and Cytokinesis: Chromosomes decondense and nuclear membranes re-form. Cleavage furrow separates the 2 cells into 4 cells. Meiosis Notes:  Haploid (1N) daughter cells - gametes. "Ready for fertilization process"  1 chromosomes from each pair is produced  Majority of cytoplasm produces a single healthy egg for females  Four sperm are produced with equal cytoplasm  Females produce ova via oogenesis  Males produce sperm via spermatogenesis  Fertilization = fusion of the 1N gametes: Always results in a 2N zygote that develops into embryo Figure 14.18: A comparison of three types of sexual life cycles (above) Figure 14.23: A comparison of Alloploidy in species hybrids and new organisms (below) Chapter 15: Inheritance and Phenotype Determination (15.1,15.4,15.5) Why Study Mendel?  Gregor Mendel was the first to demonstrate: "Principles of Inheritance"  Mendel was a monk who lived in a safe place while wars were raging at the time; encouraged to study genetics to disprove Darwin's theory of Evolution  Systematic scheme based upon an understanding of mathematics and statistics  Excellent scientific method  Blending of Characteristics: old way of thinking of inheritance was the concept of blending: thought that characteristics were added together - blending - in the new generation  Mendel applied the scientific method and mathematic analysis to show Unit Characteristics  Segregation of those characteristics  Dominance of some characteristics  Independent assortment of characteristics True-Breeding Stock  Mendel needed stocks of plants that bred in a reliable manner  Develop true-breeding stock  Produce progeny that are just like the parent with regard to characteristics  Mendel achieved true-breeding stocks by inbreeding for several years  Parental type crossed into parental type, yields parental type  Inbreeding : breed parent to progeny, sibling to sibling  Carefully chosen organism: Pisum sativum: the Garden Pea (First model organism used in Biology) Selected Crosses Produced Specific Progeny Types  Definitions:  P: parental generation of true breeders  F1: 1st filial generation: the progeny of crossing true-breeding P generation individuals that had varied in one character  F : represents the 2nd filial generation, derived from crossing the F generation to itself 2 1  One of Mendel's Crosses: Compared what we call today the phenotype, which is the outward expression of the genes  Parental Cross: Homozygous Tall (TT) and Homozygous Short (tt)  Result: All the 1 generations are tall  Demonstrates the concept of dominance Homozygotes & Heterozygotes  Alleles are different varieties of genes  Dominant alleles: capital letters (TT)  Recessive alleles: lower case letters (tt)  TT is homozygous dominant  Phenotype is dominant (Tall)  Tt is heterozygous  Phenotype is dominant (Tall)  tt is homozygous recessive  Phenotype is recessive (Short) Cross the F1generation:  1/4 of F2generation (the progeny of the F 1ross are short)  Mendel showed that the short plant bred true, so it was a parental type  That a parental phenotype disappeared and then reappeared = proved blending did not occur (masked in the F 1  The concept of unit characteristics - genes, as we now understand them = not blending Segregation of Characteristics/Chromosomal Basis of Allele Segregation  Separation of characteristics into the gametes  Seen in subsequent generation  Characteristics must segregate (separate) in the gametes  Segregation occurs in meiosis at Metaphase 1 and then at Metaphase II  Step 1: Chromosomes replicate and cell progresses to metaphase of meiosis I  Step 2: Homologous segregate into separate cells during anaphase of meiosis I  Step 3: Sister chromatids separate during anaphase of meiosis II.  Ova and sperm give different homologous chromosomes to the progeny Mendel's Concepts & Modern Terminology  Mendel had no idea of the nature of the genetic material  We know his 'characters; are the products of genes. The collection of genes (in an organism) is the genotype, or genome  A genes is positioned at a given locus (loci, plural). Physical location of a gene Alleles  Different varieties of genes  There are two possible alleles for each gene locus in a 2n (diploid) organism, i.e. 2 sets of chromosomes  If those alleles are the same, the organism is homozygous at that locus  If those alleles are different, the organism is heterozygous at that locus Punnett Squares & Test Crosses  Used to predict each generation  Allelic composition of the progeny by adding the alleles together Mendel's Laws:  Law of Dominance: In a cross of parents that are pure for contrasting traits, only one form of the trait will appear in the next generation. Offspring that are hybrid for a trait will have only the dominant trait in the phenotype  Law of Segregation: During the formation of gametes (eggs or sperm), the two alleles responsible for a trait separate from each other. Alleles for a trait are then "recombined" at fertilization, producing the genotype for the traits of the offspring  Law of Independent Assortment: Alleles for different traits are distributed to sex cells (and offspring) independently of one another Product Rule  Probability that two or more independent events (phenotype of one does not affect phenotypes of others) will occur equals the product of their individual probabilities  Example: For two heterozygous parents, what is the probability that 3 children will be homozygous recessive?  Answer: (1/4 x 1/4 x 1/4) = 1/64 probability Sum Rule  Probability that 1 of 2 or more mutually exclusive outcomes ("either/or question") will occur is the sum of the probabilities of the possible outcomes  Example: In a cross between two heterozygous (Tt) pea plants, we may want to know the probability of a particular offspring being a homozygote  (1/4 + 1/4) = 1/2 => i.e. half of the offspring are homozygotes (TT or tt) Linkage  Genes can be linked; i.e. they are on the same chromosome - same piece of DNA  Note independent assortment  Interferes with Mendelian frequencies  Linked genes are therefore easily detected: If the frequency distribution of genes in the progeny in a dihybrid cross is not Mendelian, the genes are linked. Two-Point Testcross (Thomas Morgan used the fruit fly (Drosophila melanogaster))  F (BbVv) to a homozygous recessive (male, black with vestigial wings) 1  Expect a 1:1:1:1 phenotypic ratio in the progeny, if B and V are unlinked  Instead, get close to a 2.7:2.7:1:1 phenotypic ratio  This overabundance can occur only if b and c are linked; when b and c are linked, bc and b c gametes that give rise to alternative phenotypes that can only be produced by meiotic crossover Crossover Determines the Relative Location of Genetic Loci  Crossover is assumed at equal frequency for each location along a chromosome. Crossover proportional to distance between 2 loci  Distances between loci are related to the rate of crossover => one percent=one map unit Mapping Chromosomes  If there is 48.5% crossover between Aristaless & Black body, 13% crossover between Aristaless and Dumpy wings, and 25.5% between Dumpy wings and Black body, they must be arranged as in the figure to the right. Incomplete Dominance (Figure below, right)  Heterozygotes has intermediate phenotype  Neither allele is dominant  Pink four-o'clocks: 50% of normal protein not enough to give red colour  Example: Human Phenylketonuria (PKU): Heterozygotes appear phenotypically normal, but heterozygotes have double the normal phenylalanine levels  People with phenylketonuria (no functional phenylalanine hydroxylase) can develop normally if given a diet free of phenylalanine  Normal diet contains phenylalanine, they accumulate this amino acid which becomes toxic: develop mental impairment, underdeveloped teeth and foul-smelling urine Sex-influenced inheritance  Allele is dominant in one sex, but recessive in the other  Example: Pattern baldness: Baldness allele dominant in men, but not women  Only a woman homozygous for baldness allele would be bald (or adrenal gland tumor causing high testosterone in females)  Not X-linked Role of the environment  "Norm of Reaction": Effects on environmental variation on a phenotype  Example: Genetically identical plants grow to different height in different temperatures The Fearless Gene Video  Neuro D2: gene that tells us to react to risky situations  Thrills are brought about by this gene Multiple Alleles  3 or more variants in a population  Phenotype depends on which 2 alleles are inherited  Example: ABO blood types in humans  Type AB is Co-dominance - expressing both alleles equally  Recall: Mendel studied true-breeding strains that differed with regard to only one gene  Gene Interactions - a single trait is controlled by 2 or more genes, each of which has 2 or more alleles Epistasis  Alleles of one gene mask the expression of the alleles of another gene  Often arise because 2 or more different proteins are involved in a single cellular function Polygenic Inheritance (More than 1 gene)  Example: human Height: Robert Wadlow (8'11'' tall, 400 lbs) is the tallest person in medical history for whom there is irrefutable evidence  Example: Skin colour: In humans, 3 unlinked loci. Follows expected frequency distribution for a Mendelian trait Extranuclear inheritance  Organelles (mitochondria and chloroplasts) contain their own genomes => impart phenotypes  Examples of Human Mitochondrial Diseases Epigenetic inheritance (a control mechanism, instead of a mutation)  Known as an above control over genes and chromosomes  Modification of a gene or chromosome during egg formation, sperm formation, or early stages of embryo growth alters gene expression in a way that is fixed during an individual's lifetime  Permanently affect the phenotype of the individual, but they are not permanent over the course of many generations and they do not change the actual DNA sequence  Examples: X inactivation and Genomic imprinting) X Inactivation (Example of Epigenetic inheritance)  One X chromosome n the somatic cells of female mammals is inactivated  2 lines of evidence  Barr bodies are found in female but not male cat cells  Example: Calico cat coat color pattern  In the early embryo, all X chromosomes are initially active  In each embryonic cell, random inactivation occurs for one of the X chromosomes, which becomes a Barr body  AS development proceeds, the pattern of X inactivation is maintained during cell division Genomic Imprinting (Example of Epigenetic inheritance)  Segment of DNA is imprinted  In numerous species: insects, plants, mammals  Imprinting of single genes, part of a chromosome, an entire chromosome, or all the chromosomes from one parent  Offspring distinguished between maternally and paternally inherited chromosomes  Offspring express either the maternal or paternal allele, but not both  Example: Igf-2 gene: The maternal Igf-2 is methylated and cannot be transcribed (methylation = silencing genes) Figure 15.10, 11, 14, 20, 22, 25. Table 15.1, 15.4 Chapter 18: Genetic Technology (p.441-453) Revolution in Biological Science  Mid-1970s, began with: recombinant DNA technology (putting 2 or more pieces of DNA together)  Redirect genetic activity of organisms; change DNA to make products for an organism  Techniques and approaches include: 1. DNA cloning: isolating and amplifying specific DNA sequences, both in vivo (inside) and in vitro (out of) the cell => test-tube, using PCR to replicate 2. Genomics and Proteomics: analysis of entire genomes (all genes) and proteomes (all proteins = differences between tissues in body) 3. Biotechnology: add new genes; transgenic or genetically modified organisms (GMOs) Restriction Enzymes  Hamilton Smith, Daniel Nathans, and Werner Arber (Nobel prize winners)  Bacterial "molecular scissors"  Thousands discovered  Naturally destroy non-host (bacteriophage = viruses) DNA  Defined mechanism against viruses  Cut DNA at specific base pair sequences: usually at palindromes  Palindromes: same information sequence forward and backward  How Restriction Enzymes work (See figure to right) Recombinant DNA technology  Use of laboratory techniques to isolate and manipulate fragments of DNA  Contains DNA from 2 or more sources (possibly from same organism)  Once inside a host cell, recombinant molecules are replicated to produce identical copies or clones Gene Cloning  Want copies of a gene for study or use  Obtain lots of gene product: mRNA or protein  Vector DNA as a carrier for the DNA segment to be cloned  A vector is a carrier that delivers foreign DNA into a host cell  Examples:  Bacteria, Yeast and Viruses: Plasmids are small rings of double-stranded DNA  Mammalian Cells: Engineered mammalian viruses  Plant Cells: Abrobacterium Ti plasmid  When a vector is introduced into a living cell, it can replicate making many copies (20 or more per cell)  Common vectors are plasmid or viral (viruses)  Also need the gene of interest often from chromosomal DNA digest with restriction enzymes Biotechnology  Technologies involve the use of living organisms to benefit humans  Often involve engineering  Use began about 1200 years ago with livestock domestication (first = dog)  More recently associated with molecular genetics Genetic Engineering Applications  Transgenic organisms (all) contain foreign DNA  Valuable in research; also commercial uses  Helps to identify certain genes that cause disruptions in the cell  Transgenic bacteria now produce:  Insulin for use by human diabetics  Human growth hormone (HGH) for children with insufficient HGH  Transgenic animals: by injecting the DNA into fertilized egg cells  Transgenic goats: useful proteins in their milk  Transgenic plants  Plants cells are totipotent (somatic tissues regenerate with hormonal treatments from single cell)  Genes can be introduced into somatic tissue and entire plant regenerated with hormonal treatments  Agrobacterium tumefaciens naturally integrates genes into host chromosome  Ti plasmid modified to introduce cloned genes  Kan used as a selectable marker for kanamycin resistance  Transformed cells plated on media with kanamycin (kills nontransformed plant cells) and carbenicillin (kills Agrobacterium), regenerate a single cell into a whole plant  Transgenic plants are approved for human consumption (strict government regulations)  Examples: BT insecticide, viral resistance, vitamin A (B-carotene)  Process:  Step 1: Gene of interest is inserted into the T DNA of the Ti plasmid  Step 2: The recombinant Ti plasmid is transformed into A. turnefaciens  Step 3: Plant cells are exposed to A. turnefaciens. The T DNA is transferred and incorporated into the plant cell chromosome  Step 4: The plant cells are placed in a medium containing kanamycin and carbenicillin. Karmycin kills plant cells that have not taken up T.DINA. Carbenicillin kills A. tumefaciens. The surviving plant cells are transferred to growth media that has plant hormones necessary for regenerating an entire plant. Molecular Pharming  Example: Production of medically important proteins in livestock mammary glands  Example factor IX for hemophiliacs  Certain proteins more likely to function when expressed in mammals  Post-translational modification (benefit to using mammals= bacteria cannot modify mRNA product like eukaryotes can!)  Degraded or improperly folded in bacteria  High yield in milk  Same process being used for the Montreal company producing spider silk  Process:  Step 1: Clone a human hormone gene into a plasmid vector next to a sheep B-lactoglobulin promoter. This promoter is functional only in mammary cells so that the protein product is secreted into the milk.  Step 2: Inject the recombinant plasmid into a sheep oocyte. The plasmid DNA will integrate into the chromosomal DNA, resulting in the addition of the hormone gene into the sheep's genome ("DNA microinjection")  Step 3: The oocyte is fertilized and implanted into a female sheep, which then gives birth to a transgenic sheep offspring  Step 4: Obtain milk from a female transgenic sheep. The milk contains a human hormone  Step 5: Purify the hormone from the milk Cloned Wow Cows  Cloning organisms , like "Dolly the sheep", who was cloned from the fusion of the nucleus from a mammary cell with an egg cell  Cows can produce twice the amount of milk  NAS and the University of Connecticut are putting the cow's milk through tests  So far, found that beef had higher quality proteins  More tests need to be done in order for government to approve Gene Therapy  Blease and Colleagues Performed the First Gene Therapy (to Treat Adenosine deaminase Deficiency)  More than 4,000 diseases involve a single gene abnormality  Severe Combined Immunodeficiency Disease (SCID): Fetal at early age (1 or 2 years old)  Adenosine deaminase (ADA) deficiency presents proper metabolism of nucleosides (nucleotides without the phosphate group)  Deoxyadenosine accumulates and causes toxicity to T and B cell lymphocyte  Gene therapy introduces cloned genes into living cells to cure disease.  Three treatments:  Bone marrow transplant (from a compatible donor)  Purified ADA enzyme (injections)  Gene therapy (transgenic technology)  Gene therapy (see Special Figure that is not in text, but is in printed notes)  Remove lymphocytes from girl (patient)  Treat with retroviral vector containing ADA gene  Return cells to her bloodstream  Results suggest that this first gene therapy trial may offer benefit (but patients are still also treated with ADA enzyme)  Process from diagram:  Step 1: Remove ADA-deficient lymphocytes from the patient with severe combined immunodeficiency disease (SCID)  Step 2: Culture the cells in a laboratory  Step 3: Infect the cells with a retrovirus that contains the normal ADA gene. Retroviruses insert their DNA into the host cell chromosome as part of their reproductive cycle  Step 4: Infuse the ADA-gene-corrected lymphocytes back into the SCID patient  Step 5: After injection, ADA function increases, but does not cure the patient DNA fingerprinting/DNA profiling  Applications include:  Forensics - 1986 first use in court of law to identify a suspect  Paternity testing  Identify different species  10 years ago, there was a case to show a man was shooting and eating moose meat by analyzing DNA to ensure it was moose and not cow  "Identifies particular individual using properties of his or her DNA"  Chromosomal DNA produces a series of bands on a gel  Apply Southern Blotting technique (chop apart DNA, run on gel to create bands, add probes to see bands)  Unique patter of bands provides a unique DNA fingerprint  Automated DNA Fingerprinting uses polymerase chain reaction (PCR) to amplify short tandem repeat sequences (STRs) to provide a unique pattern  Chances of mistaken identity are 1/1 billion Figures 18.8, 10, 19. Table 18.2 Chapter 20: Origin and History of Life (p.489-494)  The period from 3.5 billion years ago to the present day has seen dramatic changes in the composition of life on earth Many Environmental and biology Changes Have Occurred Since the Origin of the Earth  The geological timescale is a timeline of the Earth's history from its origin about 4.55 billion years ago, moving through four eons (and many eras). The first three eons, as seen in Figure 20.7, are "Precambrian"  The names of several eons and eras end in -zoic, meaning animal life, as we recognize many time periods based on animal life  Genetic changes in organisms can affect their characteristics, and impact their ability to survive in their environment. Changes in genetics can be fuelled by the environment; the Earth has undergone dramatic changes, which have affected the organisms living on Earth.  Environmental changes can cause extinction of a species or group of species  Environmental changes seen on Earth include the following:  Climate and temperature: Earth has undergone major fluctuations in temperature, with Ice Ages, and warmer temperatures  Atmosphere: the chemical composition of gases surrounding the Earth has changed over the years, especially with the emergence or oxygen, which has allowed for the creation of organisms to use the oxygen  Land masses: As the Earth cooled, land masses were surrounded by bodies of water. Land masses also shifted, due to continental drift. (Seen in Figure 20.8)  Floods: Floods have flooded regions of land, causing extinction of some species  Glaciation: Glaciation affects water level in oceans, and composition of species who lived on the land masses that the glaciers went across  Volcanic eruptions: Eruptions can form new islands, but can also affect global temperatures and limit solar radiation (limits photosynthetic production) and may negatively affect species near the eruption  Meteorite impacts: Meteorites that strike the Earth can cause extinction of species (dinosaurs)  One or more of the environmental changes above may cause mass extinction, which is when many species go extinct at the same Figure 20.8: Continental drift: time. This occurred at the end of five periods (5 mass extinction): Ordovician, Devonian, Permian, Triassic, and Cretaceous The relative locations of the  Geological eras are often defined by biological extinctions and continents on Earth have adaptive radiations of flora and fauna changed over the past hundreds of millions of years Fossils Provide a Glimpse into the History of Life  Fossils are the recognizable remains of past life on Earth; the scientists who study fossils are called paleontologists  The fossil record provides a record of the life forms that existed during particular geological periods  Many of the rocks seen by paleontologists are sedimentary, formed from particles of eroded older rocks. Fossils are formed when organisms are buried quickly, and the hard parts of the organisms are replaced by mineral deposits in the sedimentary rock formation over time  Paleontologists often study changes in life forms over tie by studying the fossils in various strata - the more ancient life forms are found in the lower strata, while never species are found in the upper strata  A common way to estimate the age of a fossil is by analyzing the chemical compounds found in the accompanying rock, using radioisotope dating. Radioactive isotopes are unstable and decary at a specific rate called the half-life. The half-life is the time it takes for half the isotope to decay; each isotope has its own unique half-life  Using a sample of rock, scientists can measure the amount of a given radioactive isotope and the amount of the isotope that is produced when the original isotope decays  Factors like anatomy, size, number, and environment the organisms that has been fossilized affects the fossil record. As a result, the fossil record is not comprehensive, but provides scientists with a story of the history of life Prokaryotic Cells Arose During the Achaean Eon  The Achaean (meaning "ancient") eon was a time when diverse microbial life flourished int he primordial oceans  The single-celled microorganisms of this eon almost certainly used only anaerobic (without oxygen) metabolism  Heterotrophs: find energy from organisms or materials they ea; the energy of the chemical bonds in those biological molecules of the food provides a Figure 20.10: Radioisotope dating of fossils. a) source of energy; rely on autotrophs for the production Rocks can be dated by measuring the relative of food  Autotrophs: have metabolic pathways to directly amounts of a radioisotope and its decay product harness energy from inorganic molecules or light that they contain. b) These five isotopes are particularly useful for dating of fossils  Scientists hypothesized that the first living cells were heterotrophs, in a bath of nutrient-rich organic matter. As the organic matter was exhausted, cells evolved to have the ability to synthesize organic molecules from inorganic sources, and had a growth advantage  Cyanobacteria were preserved in fossils as they produce a layered structure called a stromatolites; cynobacterial deplete carbon dioxide around them , causing calcium carbonate to precipitate over the bacterial cells, which allow them to fossilize  As oxygen was brought into the Earth's atmosphere, it enabled the formation of new aerobic (with oxygen) prokaryotic species, and the explosion of eukaryotic life forms Chapter 21: An Introduction to Evolution  Evolution is often associated with a process that involves change  Biological evolution: a heritable change in one or more characteristics of a population or species across many generations  Evolution can be viewed on a small scale (microevolution) or a larger scale (macroevolution) as it relates to the formation of new species or groups of related species  Species: a group of related organisms that share a distinctive form; can interbreed and produce fertile offspring  Population: refers to members of the same species that are likely to encounter one another and so have the opportunity to interbreed  Basic tenets of evolution were proposed by Charles Darwin  Theodosius Dobzhansky, an influential evolutionary scientist of the early twentieth century said "Nothing in biology makes sense except in the light of evolution" -- See additional reading for this  Advances in molecular genetics, like those in DNA sequencing and genomics, have revolutionized the study of evolution  Molecular evolution: refers to the molecular changes in genetic material that underlie the phenotypic changes associated with evolution 21.1 Historical Views on Evolutionary Change  Early classification systems for plants and animals began with an Englishman named John Ray in the mid- to late seventeenth century. He established a modern concept of a species, noting that organisms of one species do not interbreed with members of another and he used the species as the basic unit of his classification system  Carolus Linnaeus followed, who used the term genus to group similar organisms, extending genera (plural of genus) into orders, orders into classes, and classes into kingdoms  Baron Georges Cuvier argued against evolutionary change, because he saw organisms as integrated wholes and that a change in any one structure would upset the functional integration of the whole and the organism would fail to survive  Jean-Baptiste Lamarck suggested an intimate relationship between variation and evolution; through studying fossils he found that some species had remained the same over many years, while others had changed. He believed that over many generations, species survive by adapting to new environments; living things evolved through simple to more complex forms towards "perfection". He hypothesized that modified traits were inherited by offspring through the theory of "inheritance of acquired characteristics" (this has since been disproven through studies)  Erasmus Darwin - grandfather of Charles Darwin - knew that offspring inherited features from their parents and suggested that evolutionary change might occur as a result of competition  Charles Darwin created a theory that existing species have evolved from pre=existing species  During this time, two theories about the Earth existed: catastrophism (Cuvier) suggested that the Earth was only 6,000 years old, and catastrophic events have changed its geological structure; the other theory, uniformitarianism (Hutton), suggested that changes in Earth are directly caused by recurring events  Also during this time, Malthus found that population size of humans increases linearly due to improvements in agriculture, but our reproductive potential is exponential; as a result, famine, war, and disease will limit population growth; only a fraction of any population will survive and reproduce. This shaped Darwin's thinking  Darwin went on a venture on the Beagle from 1831 to 1836; he made many observations, but was interested in the distinctive traits of island species that would provide them with ways to better exploit their native environments (ex. Galapagos Islands finches and the change in size and shape of bills over time)  Darwin formulated his theory of evolution by natural selection by the mid-1940s  The Origin of Species - Darwin's book - spoke about natural selection; in his novel, "the theory of descent with modification through variation and natural selection" was discussed. This theory was based on 2 factors: variation within a given species, and forces of nature termed "natural selection"  During the process of natural selection, certain individuals are less likely to survive and reproduce in an environment, while others are better suited to the environment because of their traits; nature selects for those favourable traits  Over long periods of time, natural selection leads to adaption, which is an evolutionary change in which a populations characteristics change to make its members better suited to their native environment  Genetic variation is a feature of natural populations; variation may involve differences in genes, changes in chromosome structure and alterations in chromosome number. Genetic variation is caused by random mutations hat alter the composition, and not by the environment  Neo-Darwinism or the "modern synthesis of evolution" was termed to describe that within a given population of interbreeding organisms, natural variation exists because of random changes in the genetic material  If a genetic change promotes the individual's survival, natural selection will increase the prevalence of the trait in future generations 21.2 Observations of Evolutionary Change  Over the last 150 years, the research community has learned that no known concept other than descent with modification from a common ancestor can scientifically account for the diversity and unity of life on our planet; more recently by comparing DNA sequences from many species, we have gained insight into the relationship between evolution of species and the changes in the genetic material  When fossils are compared according to their age, from oldest to youngest, successive evolutionary change becomes apparent  Transitional form: provides a link between earlier species and many later species (ex. fishapod is a transitional form between fish and tetrapods  One of the best-studied examples of evolutionary change is that of the horse family; changes in horse characteristics can be attributed to natural selection producing adaptations to changing global climates  Biogeography: study of the geographical distribution of extinct and modern species; patterns of past evolution are often found in the natural geographical distribution of related species  Scientists have found that isolated continents and island groups have evolved their own distinct plant and animal communities (like the finches on the Galapagos Islands)  Endemic: Islands that have species of plants and animals that are naturally fond only in particular location; endemic island species have been most closely related to relatives on nearby islands or the mainland  Island dwarfing: the phenomenon in which the size of large animals isolated on an island shrinks dramatically over many generations; it is a form of natural selection in which smaller size provides a survival advantage, probably due to limited food  Convergent evolution: two different species from different lineages show similar characteristics because they occupy similar environments  Analogous structures/Convergent traits: Traits that are a result of convergent evolution; structures have arisen independently, because species have occupied similar types of environments on Earth  Homologous structures: Traits that are similar because of a single evolutionary origin  Selective breeding: refers to programs and procedures designed to modify traits in domesticated species; the practice associated with breeding is called artificial selection. In nature, natural selection will choose favourable traits - in artificial selection, the breeder will choose the traits (through allele selection)  Homology: refers to a fundamental similarity that occurs because of descent from a common ancestor; two species may have a similar trait because the trait was originally found in a common ancestor  Anatomical Homologies: Homologous structures are derived from a common ancestor; natural selection explains how the animals have descended from a common ancestor. In this category, vestigial structures (anatomical features that have no apparent function but resemble structures of the organism's presume ancestors) also plays a role in the evolution of the species; natural selection may eliminate such structure because of the inefficiency of producing unused structures  Developmental Homologies: Another example of homology is the way that animals undergo embyoinc development; species that differ substantially at the adult stage often bear similarities during early stages of embryonic development - temporary similarities are called developmental homologies. The can also be considered anatomical homologies seen in embryos or other developmental stages, but may not show up later in the lifespan of organisms  Molecular Homologies: When scientists examine the features of cells at the molecular level, similarities called molecular homologies are found, which indicate that living species evolved form a common ancestor or interrelated group of common ancestors. Most compelling observation of this is that modern life forms are all derived from a common ancestor through analyzing genetic sequences. First, certain genes are found in a diverse array of species. Second, the sequences of closely related species tend to be more similar to each other than they are to distantly related species Type of observation Description Fossil record When fossils are compared according to their age, from oldest to youngest, successive evolutionary change becomes apparent. Biogeography Unique species found on islands and other remote areas have arisen because the species in these locations have evolved in isolation from the rest of the world. Convergent evolution Two different species from different lineages sometimes become anatomically similar because they occupy similar environments. Selective breeding The traits in domesticated species have been profoundly modified by artificial selection practices. Anatomical Evolutionarily related species may possess homologous structures that have been modified in ways that allowed them to be used differently by each species Developmental An analysis of embryonic development often reveals similar anatomical features that point to past evolutionary relationships. Molecular At the molecular level, certain characteristics are found in all living cells, suggesting that all living species are derived from a common ancestor. In addition, species that are closely related evolutionarily tend to have DNA sequences that are more similar to each other than they are to those in distantly related organisms. Chapter 22: Population Genetics  Population genetics: the study of genes and genotypes; helps scientists to understand how underlying genetic variation is related to phenotypic variation and other issues, such as feeding ecology  Mathematic foundations come from theories developed by Darwin and Mendel 22.1 Genes in Populations  Population genetics is an extension of Darwin's theory of natural selection and Mendel's law s of inheritance, in addition to newer studies in molecular genetics  All genes in a population make up its gene pool; members of a population receive genes from their parents, then produce offspring, who will also contribute to this pool  Population: a group of individuals of the same species that can interbreed with one another; some may occupy a wide geographic range and may be divided into discrete populations  A geographic barrier may separate two or more populations on the same continent  As population sizes and locations change, their genetic composition generally changes as well  Polymorphism: refers to the phenomenon that many traits display variation within a population; phenotypic polymorphism is caused by two or more alleles that influence the phenotype of the individual that inherits them (it is due to genetic variation  A genes that exists as two or more alleles is a polymorphism gene; a monomorphic gene exists as a single allele in a population  Polymorphism can involve various changes at the molecular level: deletion of ta significant region of the gene, a duplication of the region, or a change in a dingle nucleotide (single-nucleotide polymorphism (SNP))  Allele frequencies: the frequency for an allele to appear in an offspring; uses the following equation:  Genotype frequency: the frequency for a genotype to appear in an offspring; uses the following equation:  Allele and genotype frequencies are always less than or equal to one (100%)  Hardy and Weinberg, in 1908, created the Hardy-Weinberg equation that related allele and genotype frequencies when they are not changing (p + q = 1 for alleles, p + 2pq + q = 1 for genotypes, with 2 2 homozygous dominant RR as p ,heterozygous Rr as 2pq, and homozygous recessive rr as q ).  The Hardy-Weinberg equation reflects the way gametes combine randomly to produce offspring. This equation also predicts an equilibrium of unchanging allele and genotype frequencies in a population; if a population is in equilibrium it is not adapting and evolution is not occurring. Must follow the following conditions:  The population is so large that allele frequencies do no t change through random sampling error  The members of the population mate with one another without regard o their phenotypes and genotypes  No migration occurs between different populations  No survival or reproductive advantage exists for any of the genotypes - in other words, no natural selection occurs  No new mutations occur  In reality, no population satisfies the Hardy-Weinberg equilibrium completely 22.2 Evolutionary Mechanisms and Their Effects on Populations  Microevolution: used to describe changes in a population's gene pool from generation to generation (See Table 22.1 below)  The introduction of new genetic variation into a population is an essential aspect of microevolution; new alleles from pre-existing genes arise through random mutation and new genes can be introduced into a population by gene duplication, exon shuffling, and horizontal gene transfer; however, mutations have a low rate of occurrence and are not the only driving force for microevolution  The action of evolutionary mechanisms alter the prevalence of a give allele or genotype in a population; occurs through natural selection, random genetic drift, migration, and non-random mating  "Struggle for existence" results in the selective survival of individuals that have inherited certain genotypes  The genotypes have greater reproductive success: natural selection acts to select characteristics that will allow the population to best adapt to its environment, and to survive and produce viable offspring  Darwinian fitness: the relative likelihood that a genotype will contribute to the gene pool of the next generation as compared with other genotypes; measure of reproductive success; by convention the genotype with the highest reproductive success is given a fitness value of 1.0; variation in fitness occurs because individuals with certain genotypes have greater reproductive success  Average reproductive success of members of a population is called the mean fitness of the population; over generations, as natural selection selects for certain traits, the mean fitness of the population will increase Natural Selection in Differential Reproductive Success of Individuals in a Population  Directional Selection: favours individuals consistently above or below the mean or median of a phenotypic distribution that have greater reproductive success in a particular environment  A new allele is introduced into the population by mutation and the new allele confers a higher fitness in individuals that carry it; or the population is exposed to a prolonged change in its environment and so the fitness changes to favour one genotype to promote the elimination of the other genotypes  Stabilizing selection: favours the survival of individuals with intermediate phenotypes; extreme values of trait are selected against, but this tends to decrease genetic diversity  Disruptive Selection: favours the survival of two or more different genotypes that produce different phenotypes; fitness values of a particular genotype are higher in one environment and lower in another environment while fitness values of the other genotype vary in tan opposite manner.  This form of selection occurs in populations that occupy diverse environments, so some members will survive in each environment  Disruptive selection cause by heterogeneous environments can eventually lead to the evolution of two or more different species (seen in the next Chapter 23)  Balancing selection: a type of natural selection that maintains genetic diversity in a population  This form of selection creates a situation known as balanced polymorphism or stable polymorphism, where two or more alleles in a population are kept in balance over the course of many generations  Balancing selection favours the heterozygote rather than either homozygous genotype; this is known as heterozygote advantage; however this explains the high frequency of alleles that are deleterious  Negative frequency-dependent selection: second way natural selection can produce this balancing effect; the fitness of a genotype decreases when its frequency becomes higher - rare individuals have a higher fitness and common individuals have a lower fitness Sexual Selection is a Type of Natural Selection that Directly Promotes Reproductive Success  Sexual selection: directed at certain traits of sexually reproducing species that make it more likely for individuals to find or choose a mate and engage in successful mating  Sexual selection typically affects males more than it does females; sexual selection typically affects the evolution of traits called secondary sexual characteristics that can create a significant difference in appearance between males and females  Intrasexual selection: sexual selection between members of the same sex  Intersexual selection: sexual selection between members of the opposite sex  Female choice is a type of sexual selection that results in showy characteristics in males; this can also include cryptic female choice where the female reproductive system can influence the relative success of sperm  Males closely related to the female have sperm that are less successful than the sperm of males that are more distant to the female  This inhibits inbreeding and usually occurs in species where the females can mate with more than one male  Sexual selection can sometimes be a combination of both intrasexual and intersexual selection  Sexual selection can explain traits that decrease an individual's chance of survival but increase their chances of reproducing  Sexual selection is governed by the same processes involved in the evolution of traits not directly related to sex; sexual selection can also be directional, stabilizing, disruptive, or balancing In Small Populations, Allele Frequencies Can be Altered by Random Genetic Drift  Random genetic drift: refers to changes in allele frequencies caused by random sampling error; allele frequencies can "drift" from generation to generation as a matter of change; random sampling error/deviation is observed and predicted through random events unrelated to fitness  Changes in allele frequencies caused by genetic drift happen regardless of the fitness of the individuals; random sampling error can influence which alleles are found in the gametes in a successful fertilization  Genetic drift favours either the loss or fixation of an allele (to reach 0% or 100%); the rate at which this occurs depends on the population size - more generations needed to grow in larger populations  Bottleneck effect: One way genetic drift occurs; a population size reduced dramatically by environmental factors, which randomly eliminates members from a population. Surviving members have allele frequencies that differ from those original populations, and allele frequencies drift substantially (some alleles are even lost completely). The population will return to its original size, but will have less variation than the original population  Founder effect: Occurs when a group of individuals splits off from a larger population to establish a new colony (like on an island); this differs from the bottleneck effect as it is in a different area. The founding population will be relative small and will have less genetic variation; allele frequencies may differ from those of the original population The Neutral Theory of Evolution Proposes that Genetic Drift Plays an Important Role in Promoting Genetic Change  Genetic drift does not preferential select any particular allele as it is a random process  Most of the time, genetic drift promotes neutral variation which does not favour any particular genotype  According to the neutral theory of evolution, most genetic variation is due to the accumulation of neutral mutations (usually on the 3rd base of a codon) that have attained high frequencies in a population through genetic drift; these changes do not affect the phenotype of the organism, so they are not accepted by natural selection  non-Darwinian evolution ("survival of the luckiest"): neutral mutations do no affect phenotype, so they spread throughout a population through genetic drift Migration Between Two Populations Tends to Increase Genetic Variation  Migration to a new location by a relatively small group can result in a founding population with an altered genetic composition caused by genetic drift; migration between two different established populations can also alter genetic variation  Gene flow: occurs whenever individuals migrate between populations having different allele frequencies; in nature individuals commonly migrate in both directions  Migration tends to reduce difference in allele frequencies between neighbouring populations  Migration also tends to enhance genetic diversity within a population by introducing a new mutated allele into a neighbouring population Nonrandom Mating Affects the Relative Proportion of Homozygotes and Heterozygotes in a Population  Nonrandom mating: mating with individuals in a population in a nonrandom way; in positive assortative mating, individuals with similar phenotypes are more likely to mate, which means that mating tends to increase promotion of homozygotes (due to the genotype that produces the phenotype) and decreases the proportion of heterozygotes  Nonrandom mating differs form sexual selection in that sexual selection results in a sexually dimorphic species  Individuals in nonrandom mating may also choose a mate who is part of the same genetic lineage (mating of two genetically related individuals is called inbreeding)  Nonrandom does not affect allele frequencies as no evolutionary forces are acting on it; however it will disrupt the balance of genotypes  Inbreeding increases the relative proportions of homozygotes and a decrease for heterozygotes; an inbred individual has a higher chance of being homozygous because of the higher chance its parents will give it the same allele for a gene, twice  In a natural population, inbreeding will lower the mean fitness of a population, if homozygous offspring have a lower fitness value  Inbreeding depression: as population decreases, inbreeding is more prevalent, which produces more homozygotes that are less fit, decreasing the reproductive success of a population Factors That Govern Microevolution Sources of new genetic variation * New alleles Random mutations within pre-existing genes introduce new alleles into populations, but at a very low rate. New mutations are generally deleterious, but they can be neutral or even beneficial. For alleles to rise to a significant percentage in a population, evolutionary mechanisms, such as natural selection, random genetic drift, and migration, must operate on them. Gene Abnormal crossover events and transposable elements may increase the number of copies of a duplication gene. Over time, the additional copies can accumulate random mutations and create a gene family. Exon shufflingAbnormal crossover events and transposable elements may promote gene rearrangements in which one or more exons from one gene are inserted into another gene. The protein encoded by such a gene may display a novel function and can then be acted on by evolutionary mechanisms. Horizontal Genes from one species may be introduced into another species. Such events as endocytosis and gene transfer interspecies mating may promote this phenomenon. Evolutionary mechanisms that alter existing genetic variation Natural Natural selection is the differential reproductive success of individuals in a population. This selection includes not only the survival of an individual but also its ability to reproduce. As a type of natural selection, sexual selection favours traits that increase the reproductive success of individuals. It is important to realize the distinction that natural selection acts on the individual while evolution describes changes in populations. Random Random genetic drift is a change in genetic variation from generation to generation caused by genetic drift random sampling error. Allele frequencies may change as a matter of chance from one generation to the next. This is much more likely to occur in a small population. Migration Migration can occur between two different populations that have different allele frequencies. The (gene flow) introduction of migrants into a recipient population may change the allele frequencies of that population. Nonrandom The phenomenon in which individuals select mates based on their phenotypes or genetic lineage. mating This can alter the relative proportion of homozygotes and heterozygotes that is predicted by the Hardy-Weinberg equation, but it will not change allele frequencies. Chapter 23: Origin of Species and Macroevolution  Species: a group of organisms that maintains a distinctive set of attributes in nature  The distinction between different, closely related species is often blurred in natural environments, so that it may not be easy to definitively distinguish two species  Speciation: mechanisms that promote the formation of a new species  Macroevolution: evolutionary changes that create new species and groups of species, including the diversity of organisms established over long periods of time through the evolution and extinction of many species; occurs by the accumulation of microevolutionary changes (those that occur in a single gene)  Natural selection results in the evolution of traits that promote environmental adaptation and reproductive success 23.1 Species Concepts  A single species can exist in two distinct populations, while attempting to evolve into two or more different species; time it has been since the species were first separated impacts the changes that have occurred (ex. longer time = more changes)  Biologists rely on the following potential characteristics to differentiate species: morphological traits, the ability to interbreed, molecular features, ecological factors, and evolutionary relationships  Species concept: a way to define the concept of a species and provide an approach to distinguish one species from  Morphological species concept: species can be categorized based on their physical characteristics; organisms are classified as the same species if their anatomical traits appear to be very similar (DNA sequences can be used to compare species)  Drawbacks include: difficultly deciding how many traits to consider when characterizing individuals; degree of dissimilarity that separates species is difficult to agree on; members of different species may look very similar to each other but are reproductively isolated  Biological species concept: a species is a group of individuals whose members have the potential to interbreed with one another in nature to produce viable, fertile offspring, but cannot successfully interbreed with members of another species  Difficult to determined if two populations are reproductively isolated; two species can interbreed in nature but maintain themselves as separate species; this concept cannot apply to asexual organisms  Reproductive isolation: prevents one species from successfully interbreeding with other species  Reproductive isolating mechanisms: mechanisms that prevent interbreeding between different species; merely a consequence of genetic changes that occur because a species becomes adapted to its own particular environment  Prezygotic isolating mechanisms: prevent the formation of a zygote  Postzygotic isolating mechanisms: blocks the development of a viable and fertile individuals after fertilization has taken place  Interspecies hybrid: when two different species do produce an offspring  In hybrids, a crossover may occur in the region that is inverted in one species but not the other - this will produce gametes with too little or too much genetic material and so offprings from hybrids will have developmental abnormalities 23.2 Mechanisms of Speciation  Formation of a new species (speciation) is caused by genetic changes in a particular group to make it different from the species from which it was derived  Interspecies mating, changes in chromosome number, and horizontal gene transfer can cause new species to arise  Species are a consequence of adaptation to different ecological niches  Species of sexually reproducing organisms arise via reproductive isolation  Anagenesis: a single species is transformed into a different species over many generations; evolutionary mechanisms cause the characteristics of the species to change  Cladogenesis: involves the division of a species into two or more species; one reason is geographic isolation: if one or more individuals move to a new location that is geographically isolated from the original population, evolutionary mechanisms will operate independently on the two populations  Sexual reproduction is a barrier to cladogenesis, but not to anagenesis; a population will evolve as a single unit if members can successfully breed with one another; cladogenesis begins when gene flow becomes limited between two or more populations  Allopatric speciation: occurs when some members of a species become geographically separated from the other members; separation may be caused by slow geological events that produce geographic barriers  Can also occur through the founder effect, where a small population moves to a new location that
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