BIOA01 Module 1 PDF

Evolution Evolution properties: - Things evolve - Evolution usually happens gradually - Speciation occurs - All species share common ancestry - Much of evolutionary change was caused by natural selection Chapter 1.4 Variety in populations provides the raw material for evolution: The p...

Evolution Evolution properties: - Things evolve - Evolution usually happens gradually - Speciation occurs - All species share common ancestry - Much of evolutionary change was caused by natural selection Chapter 1.4 Variety in populations provides the raw material for evolution: The prince of natural selection; when there is variation within a population of organisms, and when that variation can be inherited, the variants best suited for growth and reproduction in a given environment will contribute excessively to the next generation. Darwin - farmers have used this principle for thousands of years to select crops with high yield or improved resistance to water shortage and disease. Selection under domestication by Charles Darwin: the development of dog breeds from terriers to huskies Environmental variation: variation among individuals is sometimes due to differences in the environment. ○ Some apples have better exposure to sunlight; some hidden in shade Genetic variation: differences in the genetic material that’s transmitted from parents to offspring ○ Differences among individuals’ DNA can lead to differences among the individuals’ RNA and proteins, which affect the molecular functions of the cell and can lead to physical differences we can observe ○ Mature apples differ in taste and colour; yellow, green, red apples In all sexual organisms, fertilization produces unique combinations of genes which examples why siblings may be so different Environmental factors such as UV radiation can damage the DNA How evolution works: the genetic makeup of a population changes over time Evolution can be depicted as a tree showing a nested pattern of relatedness among species Evolutionary theory predicts that primates should show a pattern of similarity Eukaryotes: large multicellular organisms  ○ Humans Eukarya is now thought by many biologists to have originated from a partnership between an archaeon and a bacterium Evolution can be studied by means of experiments Lenski: grew populations of the common intestinal bacterium E. Coli in a container with glucose as the only source of food. He hypothesized any bacterium with a mutation that increased its ability to use glucose would grow and reproduce at a faster rate than other bacteria in the population. His experiment concludes that E.COli evolved an improved ability to metabolize glucose over time. ○ Bacteria became adapted to living in an environment in which glucose was limiting Chapter 20.1 Adelie penguin is two to three times more genetically variable than humans Two factors that contribute to the pheotype: an individual's genotype, which is the set of alleles possessed by the individual, and the environment where the individual lives Population genetics is the study of patterns of genetic variation Species: group of individuals that’re capable of sharing alleles with one another through reproduction Alleles: different versions of genes, one of each from biological parents Gene pool: all the alleles present in all the individuals species ○ Skin colour, hair type, eye colour Population genetics: study of variation in natural populations ○ The study of patterns in genetic variation in populations Mutation and recombination are the two sources of genetic variation Genetic variation has two sources: mutation generates new variation, recombination followed by segregation of homologous chromosomes (pairs of chromosomes inherited from each parent) during meiotic cell division shuffles mutation to create new combinations Both mutation and recombination result in new alleles Somatic mutations: occur in the body’s tissues in nonreproductive cells  ○ Only affects the cells descended from the one cell in which the mutation originally arose so it only affects that individual. ○ Somatic mutations in skin cells can cause cancer but not passed down to next generation Germ-line mutations: occur in the reproductive cells ○ They are passed onto the next generation and appear in every cell of an offspring Deleterious mutations: harmful to an organism Advantageous mutations: can increase chances of survival, reproduction Chapter 20.2 To understand patterns of genetic variation, we require information about allele frequencies Allele frequency is the proportion, that consists of a specified allele Fixation: process by which one allele replaces all the other alleles in a population Allele is fixed means there is only 1 allele for that gene in the population (frequency is 100%) Question ex: DNA sequences from a population of 500 mice. 800 G’s. what is the frequency of the T allele ○ Ans: 500 x 2 = 1000 * x2 bc each individual has two sequences ○ 800 G’s so 1000 - 800 = 200 ○ Therefore the frequency of T allele is 200/1000 Early population geneticists relied on the observable traits and gel electrophoresis to measure variation: We cannot always observe variation by looking at physical traits as we do with pea plants because of 1) large number of genes and 2) the phenotype is a product of both genotype and environment Human blood groups were one of the early example of a trait encoded by a single gene with multiple genes ○ Red blood cells have molecules on their surfaces that determine their blood type ○ Phenotype is the blood type DNA sequencing is the gold standard for measuring genetic variation Gel electrophoresis silent mutation that change DNA sequence can be spotted but not the encoded amino acid Lecture notes ❖ Every generation a new environment is experienced ❖ Individuals do not evolve ❖ Fruit Flies diversify into many different species ❖ Penicillin: antibiotic Important to humans since humans died of illness Compound is from penicillium Has evolved to defend against bacteria After 4 years of usage, increased 14% of resistance during the War ❖ Microevolution: Change within a species Driven by natural selection Depends on heritable variation in genetics of a population Natural selection forces can vary overtime ❖ Qualitative variation: Characteristics with distinct state Beetles have 2 gene types to indicate if they are red or black ❖ Quantitative variation Controlled by multiple genes Sorting from shortest to tallest in a room ❖ Phenotype is dictated by genetics, but the environment also plays an effect ❖ New alleles (mutations) can cause evolution Chapter 20.3 Evolution is a change in allele or genotype frequency over time: At genetic level, evolutio is a change in frequency of an allele or a genotype from one generation to the next  Evolution may occur without allele frequencies changing The Hardy-Weinberg equilibrium describes situations in which allele and genotype frequencies do not change Allele and genotype frequencies change over time only if specific forces act on the population Hardy-Weinberg equilibrium: a state in which allele and genotype frequencies do not change over time, implying the absence of evolutionary forces ○ A population's allele and genotype frequencies are constant, unless there is some type of evolutionary force acting upon them ○ Specifies the relationship between allele frequencies and genotype frequencies when several conditions are met A population that is in Hardy-Weinberg equilibrium meets these conditions: 1. There is no difference in the survival and reproductive success of individuals with different genotypes (no natural selection) i. Given 2 alleles A and a, where a recessive mutation is lethal (all aa individuals die). In every generation, there is a selective elimination fo a alleles meaning it will slowly decrease over time ii. Selection: elimination of mutations in a population of organisms 2. The population is sufficiently large to prevent sampling errors (large population size/no genetic drift) i. Small samples are often more misleading than large ones ii. Flipping a coin 1000 times you’d expect 50/50, but flipping it 5 times you’d expect 80% heads 20% tails iii. Chance plays a bigger role in small samples than large ones iv. Genetic drift: they survive due to luck caused by natural events usually small populations are affected 1. Founder effect: small group of population is separated from the rest of the population 2. Bottleneck effect: population is reduced in size due to natural disasters, habitat loss v. Gene flow: transmission of genes across populations 3. Populations are not added to or subtracted from by migration (no gene flow) i. Change in the allele frequencies of a population due to movement between populations ii. First population with only A alleles and second population with only a alleles. If theres a sudden influx of individuals from the second population into the first, the frequency in A in the first population will decline in contrast to the number of immigrants as a alleles enter the population 4. No mutation i. If A alleles mutate into a alleles, we see changes in the allele frequencies over the generations, meaning evolutionary change is occurring 5. Individuals mate at random (random mating) i. Mate choice must be made without regard to genotype ii. An AA homozygote, when offered a choice of mate, must choose at random The Hardy-Weinberg equilibrium relates allele frequencies and genotype frequencies P = frequency of A Q = frequency of a P+q=1 If no a alleles are present, then q=0 and p=1 Hardy-Weinberg equilibrium predicts genotype frequency from allele frequencies, and vice versa AA = p^2 Aa = 2pq aa= q^2 No a alleles present, frequency of a is 0, allele frequency of A is 1 and genotype frequency of AA in the population is 1. Therefore all the genotypes in the population are AA ○ These relationships hold only if the Hardy-Weinberg frequencies are met The Hardy-Weinberg equilibrium is the starting point for population genetic analysis The Hardy-Weinberg equilibrium provides a means of converting between allele and genotype frequencies, we can conclude that something interesting is happening in a population from an evolutionary perspective When we find a population whose allele and genotype frequencies aren’t Hardy-Weinberg equilibrium, we can predict that evolution has occurred in that population ○ Helps figure out whether the population is subject to Selection: survival and reproduction or elimtion of individuals with certain genotypes Genetic drift: when chance events cause changes in frequencies of alleles in a population Migration Mutation Nonrandom mating Given allele frequencies, calculate genotype frequencies: ○ Frequency of homozygous dominant individuals is determined by p^2 ○ The frequency of homozygous recessive individuals is determined by calculating q^2 ○ Frequency of heterozygous is 2pq Chapter 20.4 Natural selection brings about adaptations Darwin first showed that species are not unchanging, but have evolved overtime. Second, he suggested natural selection brings about adaptation Natural selection has deep implications ○ 1st observation: Members of a species differ from one another, theres variation among one species ○ 2nd observation: Some of natural selection’s variation is heritable ○ 3rd observation: In nature individuals compete for resources. Recognized by Darwin and Wallace ○ 4th observation: Darwin and Wallace stated that those that are best adapted would most likely survive and reproduce Fitness describes how well an individual survives and reproduces in a particular environment Fitness: measure of the ability of an individual to survive and reproduce in a particular environment ○ A desert plant is more efficient at minimizing water loss than another plant that's new to the environment Darwin recognized that subtle shift in the frequencies of alleles could lead to major changes over long periods of time The Modern Synthesis combines Mendelian genetics and Darwinian evolution Darwinian evolution addresses the change over time of the genotype of populations Ronald Fisher: realized that instead of a single gene dictating a trait like human height, several genes could contribute to the trait Modern Synthesis: combination of Darwin’s theory of natural selection and Mendelian genetics Natural selection increases the frequency of advantageous mutations and increases the frequency of deleterious mutations Positive selection: increases the frequency of a favourable allele Negative selection: reduces the frequency of a deleterious allele ○ Heterozygous mutation has no effect Balancing selection maintains two or more alleles in a population Natural selection that maintains two or more alleles of a given gene in a population ○ Members of the same species that live in different environments. In the species as a whole, both alleles are maintained by natural selection at high frequencies Heterozygous advantage: form of balancing selection where the heterozygote’s fitness is higher than the homozygotes ○ Malaria ○ Heterozygous individual (Aa) have an advantage over homozygous individuals (AA and AS) Natural selection can be stabilizing, directional or disruptive Instead of following individual mutations, we can examine the changes over time in a specific trait of an organism ○ Looking at the evolution of height, despite not knowing the genetic basis When looking at natural selection from focusing on one specific trait, we can see 3 types of patterns 1. Stabilizing selection: maintains the status quo and acts against extremes, acts in favour of reliable phenotypes i. Human birth rate – affected by a number of factors such as baby weight (being too small = low survival changes, being too large = complications to the mother) 2. Directional selection: leads to change in a trait over time. Acts in favour of one extreme and against the other. Compares TWO extremes i. Galapagos Islands – severe drought in 1977 killed a significant amount of vegetation that provided food for one island’s seed-eating ground finches, Geospiza fortis. Since plant species that produced big seeds survived better in drought conditions, the average size of seeds available to the birds increased ii. One survives better than the other  3. Disruptive selection: operates in favour of extremes and against reliable phenotypes i. Apple maggot flies – originally fed on fruit of hawthorn trees, but these flies have become pests of apples as well about 150 years ago. Lead to one group feeding on apple trees and the other on hawthorn trees Selective pressure: full set of environmental conditions that influences the evolution of a population by natural selection Artificial selection is a form of directional selection Farmers and breeders use selection to improve livestock and crops aka artificial selection In artificial selection the breeder typically has a goal in mind, such as breeding faster racehorses, however, natural selection in contrast has no goal Sexual selection increases an individuals reproductive success Darwin wrote “the sight of a feather in a peacock’s tail, whenever I look at it it makes me sick” ○ Tail is expensive to produce ○ Sexual selection: promotes traits that increase an individual's access to reproductive opportunities ○ Intraseuxal selection: interactions between individuals of one sex, competing with each other for access to the other sex Males have large sizes, horns, fighting ability ○ Intersexual selection: interaction between males and females, and females choosing among the males ❖ Qualitative variation: looking for discrete categories Ladybugs with black and red shells ❖ Genotype frequency: the percentage of individuals in a population with a specific genotype Dominant – AA Heterozygous – Aa Recessive – aa ❖ Allele frequency: percentage of all copies of a certain gene in a population that carry a specific gene A or a Example: ❖ Snapdragons Heterozygotes are a different colour than dominant and recessive trait  Dominant = red Heterozygous = pink Recessive = white In a sample of 1000 individuals has a total of 2000 alleles Genotype divided by number of individuals = genotype frequency Total number of alleles = 2 x number of individuals ; dominant trait Total number of alleles = 1 x number of individuals ; heterozygous trait Total number of alleles = 0 x number of individuals ; recessive trait Calculating allele frequency of a sample = adding total number of total number of alleles → should equal to the number of individuals x 2 from step 1 Number of alleles / number of alleles in the SAMPLE ◆ P + q = 100% Allee frequency helps determine the commonness or rareness of a population Since we didn't predict the offspring generation using HW, therefore the population is evolving b/c there were more white flowers than predicted ❖ Agents of microevolutionary change: Heritable change in DNA Gene flow: change in allele frequencies as individuals join a population and reproduce Genetic drift: random changes in allele frequencies caused by chance events Natural selection: reproduce individuals with different genotypes Nonrandom mating: choice of mating based on their phenotypes and genotypes ❖ Evolutionary mechanisms: Selection: adaptation based on negative, positive or balancing selection Genetic drift: small population size, fixation of one allele so its either aa or AA Migration: input of 1 allele so population is one of the two Mutation: Nonrandom mating: inbreeding Chapter 20.5 Genetic drift is a change in allele frequency due to chance Genetic drift: the random change in allele frequencies from generation to generation ○ Dramatically affects small populations  ○ Bottleneck effect: natural events causing reduction in population size of a species ○ Founder effect: few individuals arrive on an island and colonize it Genetic drift does not result in traits like adaptations the way natural selection does ○ Alleles whose frequencies are changing as a result of drift don't affect an individual's ability to survive or reproduce Genetic drift has a large effect in small populations Impact of genetic drift depends on population size ○ Small populations = result in fixation or extinction of an allele in a few generations ○ Large populations = less dramatic, after 100 generations of a large population no simulation results in extinction or fixation ○ Flipping coins – small sample of coin tosses we can expect 50:50 ratio Migration reduces genetic variation between populations Migration: movement of individuals from one population to another Gene flow: movement of alleles from one population to another Two isolated island populations of rabbits, one white, other black. Bridge is built between the island, migration occurs. Overtime black alleles enter the white and vice versa. Over time the allele frequencies of the two populations become the same Mutation increases genetic variation Without mutation, there would be no genetic variation nor evolution Nonrandom mating alters genotype frequencies without affecting allele frequencies Process results in certain phenotypes to increase and others to decrease Does not add new alleles to the population, so genotype frequencies change but not allele frequencies ○ Genotype frequency: determines how commonly a single phenotype occurs among a sample population ○ Allele frequency: percentage of all copies of a particular gene in a population carrying a specific allele Inbreeding: mating occurs between close relatives Chapter 20.6 Molecular evolution: DNA evolution, which results in genetic diversity of populations Members of one species cannot exchange genetic material with members of another species ○ Humans and chimpanzees – recent common ancestor lived about 6-7 million years ago and have been genetically isolated from each other for about the same time The molecular clock relates the amount of sequence difference between species and the time since the species diverged The extent of genetic difference between two species is a function of the time they have been genetically isolated Molecular clock: the extent of genetic difference in a gene in two taxa is a reflection of the time since the taxa shared a common ancestor ○ Clock is set using dates from the fossil record The rate of the molecular clock varies Molecular clocks are useful for dating evolutionary events like the separation of humans and chimpanzees The proteins that wrap DNA to form chromatin are encoded by histone genes, which represent the slowest molecular clock. Pseudogene: a gene that is no longer functional Lecture 5: Darwin ❖ Sexual selection always favours traits that increase an individual's access to reproductive opportunities ❖ Natural forces are always changing ❖ Al-Jahiz: theorized nature and the environment Identified species develop new traits for survival in different environmental conditions ❖ Geology contribute through documentation of fossil record ❖ Comparative morphology revealed structural similarities in ‘dissimilar’ anatomies ❖ Vestigial structures: currently useless structures Have wings but don't fly ❖ Stratification: different fossils in different layers ❖ Paleobiology: study of ancient organisms ❖ Catastrophism: theory of fossil formation by catastrophe ❖ Lamarck: stated species change time and pass on changes, organisms respond to environment, hypothesize mechanisms However, he hypothesized an incorrect mechanism for evolution ❖ Galapagos island had very strange animals ❖ Lyell: how earthquakes occur, etc ❖ Darwin was against racism, but he was sexist Chapter 22 Evolution produces 2 distinct but related patterns ○ 1. Nested pattern – found among species on Earth today ○ 2. Historical pattern of evolution recorded by fossils Chapter 22.1 A monophyletic group consists of a common ancestor and all its descendants Groups = taxa Monophyletic: describes groupings that include all the descendants of a single common ancestor that is not shared with any other species or groups of species aka clade ○ Amphibians are monophyletic – bc all the groups classified as amphibian share a common ancestor not shared by any other taxa ○ Is the most accurate way to map the evolutionary path taken by a group since its origin Phylogeny: shows both evolutionary history and relatedness of groups of organisms Paraphyletic: describes groupings that include some but not all of the descendants of a common ancestor. Includes some descendants of a common ancestor ○ Tetrapods are not considered fish even though they descended from the common ancestor of fish – the fish group is therefore paraphyletic Polyphyletic: groupings that do not include the last common ancestor of all members. Groups are designated based on the independently evolved traits ○ Clustering bats and birds together as flying tetrapods results in a polyphyletic group bc wings evolved independently in the two groups and their common ancestor did not have wings To identify which group of the 3 it belongs to, ○ 1 cut = monophyletic group  ○ 2+ cuts = paraphyletic or polyphyletic groups Taxonomic classifications are information storage and retrieval systems Taxonomy: classification of organisms ○ Purpose is to recognize and name groups of individuals as species then to group closely related species into more inclusive taxonomic groups Carolus Linnaeus: introduced to modern taxonomic groupings ○ Genus: group of closely related species Family: closely related genera belong to larger, more inclusive branch of the tree Order: closely related families ○ Class: formed by order Phylum: formed by class, has a distinct body plan Kingdom: group of closely related phyla Domains: three largest limbs ○ Eukarya, bacteria, archaea Chapter 22.2 Homology is similarity by common descent Character states: observed condition of a character ○ Arrangement of petals on a flower Homology: similarity that results from shared ancestry ○ Mammals and birds produce amniotic eggs – was apart of the common ancestor Analogy: similar characters that evolved independently in different groups as a result of similar selection pressures – results of convergent evolution ○ Analogous organisms may look alike but have involved on their own ○ Wings in birds and bats – wings evolved independently and were not present in their common ancestor ○ Convergent evolution: organisms that are not closely related evolve similar features of behaviours Hedgehogs and Tenrec are very distantly related, yet hedgehogs are more closely related to zebras than to tenrecs. Tenrecs are more related to elephants than to true hedgehogs Shared derived characters enable biologist to reconstruct evolutionary history Homologies do not help to identify sister group relationships Synapomorphies: a shared derived character between some members of a group; the basis of cladistic phylogenetic reconstruction. ○ type of homology useful in phylogenetic trees because these characteristics are shared by some, which is useful to construct a true phylogenetic tree ○ Change from 5 toes to a single toe → the hoo → in the ancestor of horses and donkeys Therefore the hoof is a synapomorphy that reveals horses and donkeys are sister groups The simplest tree is often favored among multiple possible trees Parsimony: provides the simplest explanation of the data by minimizing the number of independent origins of traits shared by different species. Choosing the simpler of two or more hypothesis to account for a given set of observations ○ Trees with fewer character changes are preferred than ones with more changes Molecular data complement comparative morphology in reconstructing phylogenetic history Construction of phylogenetic trees rely on molecular data ○ Amino acids at particular positions in the primary structure of a protein can be used for the purpose of constructing molecular data Fewest differences in organisms are the most closely related More distantly related species show a big number of differences in DNA sequence Phylogenetic trees can help to solve practical problems Sequences of changes on a tree from root to its tips tells us the evolutionary changes that have occurred over time Used in COVID-19 helped scientists understand the origins of the virus Chapter 22.3 Fossils: remains of once-living organisms, preserved thru time in sedimentary rocks ○ Provide direct documentation of ancient life Fossils provide unique information Provides info that cannot be obtained from phylogenetic trees ○ Allows to date key events in evolutionary history ○ Relationship between birds and crocodiles Fossils provide a selective record of past life Fossilization requires rapid burial ○ If not, remains of organisms are recylyced by biological and physical processes, and no fossil forms Organisms that lack hard parts leave a fossil record in 2 ways: ○ 1. Leave tracks and trails as they move about to burrow, called trace fossils ○ 2. Molecular fossils: sterol, bacterial lipid that is resistant to decomposition and can be preserved in sedimentary rocks. Documents organism that rarely form fossils Proteins, cholesterol Rarely, unusual conditions preserve fossils of unexpected quality; animals without shells, delicate flowers or mushrooms ○ During the Cambrian Period, sedimentary rock formation called the Burgess Shale accumulated on a deep seafloor covering what is now British Columbia. ○ Messel Shale – now known as Germany Geologic data indicate the age and environmental setting of fossils Fossils record the evolution of life on Earth Geologic time scale: series of time visions that mark Earth’s long history Layers of fossils in sedimentary rocks can tell us some rocks are older than other ○ Preserves information about the environment in which they formed Radiometric dating: uses the decay of radioisotopes Fossils can contain unique combinations of characters Phylogenies built for characters of modern animals show all land vertebrates from amphibians to mammals are descended from a common ancestral fish Archaeopteryx: fossil organism that illuminates the transition from dinosaur to bird Tiktaalik: fossil organism that preserves a stage in the transition from a fish to a terapod Rare mass extinctions have altered the course of evolution Animal diversity has increased than it's ever been in the past, shown in Sepkoski’s diagram ○ Mass extinction: earth experienced a sudden and large loss of species Shape the ecological landscape by removing dominant organisms Chapter 22.4 Phylogeny and fossils complement each other To build phylogenetic trees we use: anatomy, physiology, cell structure, DNA sequence ○ Lacks evidence of extinct species, environmental context of the species Fossils records has strengths that other ways cannot prove: ○ Link between birds and crocodiles runs thru dinosaurs Fossils and phylogeny show that the deep history of life is microbial Phylogenies make a clear prediction: deepest node in the tree of life marks the divergence of bacteria and archaea Geological record indicates microbial communities thrived on earth more than 3 billion years before animals first evolved Cambrian explosion: rapid animal diversification; record early evolution of anthropods, mollusks, fish Mesozoic era: witnessed major evolutionary innovations on land and water ○ Frogs, mammals, birds, lizards, turtles originated during this time period Cenozoic era: mammals, birds and lizards survived this extinction When plants colonized land surface, they changed the physical character of landscapes, while providing a major source of food for emerging land animals Phylogenetic analysis shows that mammals were derived from reptiles Lecture 7: 1. Predictions based on evolution: We should see evidence in the fossil record  Earliest traces of life on earth should be simple forms, later should be more complex forms ❖ Premineralization: organism is buried, filled with mineral rich waters. Turns tissue to stone ❖ Radiometric dating from isotope half-life provides absolute age 1. Recent - (50000 years) – Carbon (events that occurred more recent) Level of C14 in plants and animals when they die approx. = the level of C14 in this atmosphere at that time 2. Older - (more than million years) – (uranium – lead) Uranium – 235/238 ❖ Earliest life form detected on earth: Cyanobacteria → appeared 3.5 billion years ago 2. We should see change in species or morphology thru the fossil record We should sometimes see lineage dividing into two or more in the fossil record Planktonic diatom Rhizosolenia, samples from deep sea boreholes Marsh’s reconstruction of horse evolution 3. We should see transitional forms Modern groups should connect with their common ancestors Transitional forms show the intermediate states between an ancestral from its descendants Archaeopteryx ; dinosaur → bird Tiktaalik ; fish → tetrapod 4. We should see evidence of retrodictions and vestigial characters Retrodiction: something that makes sense only in light of evolution, but is not predicted by evolution Lack of mammals, amphibians and freshwater fish on oceanic island such as Galapagos Island Mammals in Madagascar Vestigial characters can have dead genes Humans have genes that make vitamin C but we can’t 5. We should be able to see evidence of natural selection Lecture 8: ❖ Polytomy: the process of dividing the branch nodes into more than three parts ❖ Pleiotrophy: one gene affects multipel traits ❖ Phylogenetic trees show branch order (in time). When the branch ends, means extinction. Therefore, more accurate than cladograms. ❖ Characters must be independent for use in classification 1. Independent trait cannot have phenotypic variation The environment shouldn't change the traits 2. Independent traits must be independent ❖ Vicariance: a lineage splits due to ecological geological events  Breakup of continents ❖ Phylogenies have applications: 1. Enhances our understanding of evolution 2. Control agriculture pests and diseases 3. Identify endangered species, manage wildlife 4. Select plants and animals for research ❖ Homologous: similar origin, same function ❖ Analogous: different origin, same function ❖ Types of traits used to construct phylogenies: 1. Morphological 2. Developmental 3. Paleontological 4. Behavioural 5. Molecular Disadvantages: base changes may have evolved independently, with only 4 states in nucleotides and 20 in amino acids Chapter 21 21.1 Speciation: process whereby new species are produced Species are repdoutively isolated from other species BSC: Members of different species are reproductively isolated from one another ○ Based on the sexual exchange of genetic information Species are groups that can potentially breed ○ Asian elephant living in Sri Lanka and India. Same species but dont have the chance to mate due to being geographically separated The BSC is more useful in theory than in practice To use the BSC, you would need to test whether they are capable of producing fertile offspring Morphospecies concept: the idea that members of the same species usually look like each other more than like other species ○ Has been extended now – members of the same species have similar DNA sequences that are distinct from those of other species  Members of different species can also look quite similar ○ Agrodiaetus butterflies Cryptic species: species consist of organisms that has been traditionally considered to belong to a single species bc they look similar, but end up belonging to twos species bc of differences in the DNA sequences The BSC does not apply to asexual or extinct organisms BSC is useful, but it also overlooks some organisms ○ Does not apply to asexual organisms such as bacteria ○ True asexual organsism do not fit the BSC but some asexual species do (conjucation) Hybridization complicates BSC Hybrid offspring: two groups may be reproductively isolated, while in the other location, they interbreed ○ Towhee species – in some areas they interbreed, in other locations they do not ○ Common among plants Niche: the role a species plays in their community Ecological species concept: ther is a one-to-one correspondence between a species and its niche Phylogenetic species concept: highlights that members of a species all share a common ancestry and a common fate ○ All spsecies must be descended from a single common ancestor ○ Useful for asexual species Species change over time making it difficult to come up with a single comprehensive and agreed-upon concept of a “species” 21.2 Prezygotic: isolating factors before the fertilization of an egg Postzygotic: isolating factors after fertlization Prezygotic isolating factors occur before egg fertlization Plants and animals can be isolated in geographic isolation or ecological isolation ○ Polar bears and grizzly bears – closely related enough to produce fertile offspring in zoos, but geographically isolated in the wild Temporal isolation: individuals are reproductively active at different times ○ Plant species may flower at different times of the year  Behavioural isolation: individausl only mate with other individausl based on courtship rituals, songs etc Gametic isolation: incompatibility between the gametes of different individuals Mechanical isolation: incompatibility of genatilia Postzygotic isolating factors occur after egg fertilization Genetic incompatibility: similarities between two organisms such as different number of chromosomes ○ Mules are infertile caused by the horse-donkey hybrid Prezygotic factors are more efficient than postzygotic factors Both prezygotic and postzygotic factors cause difficulties to gene flow 21.3 Speciation is a by-product of the genetic divergence of separated populations If a single population is split into two populations that are isolated from each other, different mutations appear by chance in the two populations Partially reproductively isolated: they are not truly separate species, but the genetic differences between them are extensive enough that the hybrid offspring they produce have reduced fertility compared to the offspring produced by crosses between individuals within each population Allopatric speciation results from the geographic separation of populations Allopatric: populations that are geographically separated from each other Subspecies: allopatric populations that have yet to evolve even partial reproductive isolation but that have acquired population-specific traits ○ Sri lankan Asian elephants, subspecies elephas maximus maximus, are generally larger and darker than their indian counterparts, subspecies elephas Maximus Dispersal and vicariance can isolate populations from each other 2 ways in which populations may become allopatric  Dispersal: some individuals colonize a distant place, such as an island, far from the source population a. First finches arriving in the Galapagos islands from South America b. Peripatric speciation: A few individuals from the mainland population disperse into a new location remote from the original population and evolve separately. Changes happen faster. Vicariance: a geographic barrier (change in environment) arises within a single population, separating it into two or more isolated populations a. Seal levels rose at the end of the most recent ice age, and new islands formed along the coastlines. Adaptive radiation: unusual rapid evolution diversification in which natural selection drives the rate of speciation within a group, causing a new species adapted for specific niches Co-speciation occurs in response to speciation in other species Co-speciation: a process in which two groups of organisms speciate in response to each other and at the same time Speciation can occur without completely physically separating populations ○ Sympatric: populations that are in the same geographic location Plants/palm trees on Lord Howe Island Gene flow does not affect the two populations' divergence because the hybrid individuals do not survive to reproduce. Speciation can occur instantaneously Instantaneous speciation: speciation that occurs in a single generation ○ Caused by hybridization between two species in which the offspring are reproductively isolated from both parents Animals cannot handle double diploid, but plants can ○ Polyploidy: Multiple chromosome sets are common in plants ○ Allopolyploids: produced from hybridization Speciation can occur with or without natural selection 2 ways natural selection can be involved in speciation: sympatric and allopatric speciation Speciation can occur fully due to genetic drift, where natural selection has no role For populations to genetically diverge from one another, gene flow between the must be limited Lecture 10 ❖ Both species need to be living in the same geographic space ❖ Populations recently diverged is thru allopatric ❖ Biogeography can tell us how colonization can range-splitting events occur ❖ Dispersal: when a population moves to a new habitat, colonizes it, and forms a new population ❖ Autopolyploidy: chromosome duplications within a species ❖ Allopolyploidy: chromosome duplications between species, resulting in hybrid species Diploid wild what T. Monococcum (elkorn) has two sets of 7 chromosomes. T.monococcum hybridized with another species that has the same # of chromosomes Hybrid offspring became sterile, whereas the plans with 28 chromosomes were fertile ❖ Chromosomal arrangement: leads to higher rates of protein evolutionary divergence Inversions - rearrangement within itself Translocations – exchange between non-homologous chromosomes Deletions - mutations leading to loss of nucleotides Duplications – part of a chromosome is duplicated ❖ When prezygotic isolation does not exist, populations may successfully interbreed ❖ Introgression: gene flow occurs then may erase distinctions between the two populations ❖ Reinforcement: staying with ur population to produce successful offspring Chapter 25 25.1 Eukaryotoes mainly rely on an internal scaffolding of proteins to organize the cell, mostly microtubules composed of the protein tubulin and microfilaments of actin ○ Nucleus: separates transcription and translation in eukaryotes Membrane-bound nucleus that houses DNA, creating separate cellular compartments for transcription and translation is what distinguishes a eukarytoic cell from a prokaryotic cell ○ Cytoskeleton: enables cells to change shape by remodeling quickly Endomembrane system: includes nuclear envelope, an assembly of membranes that runs thru the cytoplasm called the endoplasmic reticulum and golgi apparatus Phagocytosis: form of endocytosis in which eukartoics cells surround food particles and package them in vesicles that bud off from the cell membrane Eukaryotic cells, energy metabolism is linked to cell structure Eukaryotes are limited in the ways they obtain carbon and energy  Sexual production in eukaryotes involved meiosis and the formation of gametes and the subsequent fusion of gametes during fertilization ○ Each gamete has a combinaitonof alleles different from other gametes ○ Fertilization, new combinations fo genes are brought together by the fusion of gametes ○ Meiotic cell design results in haploid cells (one complete set of chromosomes) ○ Sexual fusions result sin diploid cells (two complete sets of chromosomes) 25.2 Symbiosis led to the origin of chlorplasts ○ Symbiosis: a close interaction that has evolved between species that live together ○ Endosymbiosis: symbiosis in which one partner lives within the other Biologists agreed chlorplasts originated from endosymbiotic cyanobacteria only once Marezhkovsky’s observations: stated chlorplasts originated as symbiotic cyanobacteria that thru time became permanently incorporated into their hosts Chlorplasts have their own DNA Mitochondria are also descended from bacteria Originated as proteobacteria Both chloroplast and mitochondria originagted thru endosymbiosis 2 hypothesis for the origin of the eukaryotic cell ○ 1. Host for mitochondria-producing endosymbiosis was itself a true eukarytoic cell with a nucleus, cytoskeleton and endomembrane system subsequent engulfment of proteobacterium led to the evolution of mitochondria ○ 2. Infolding – The eukaryotic cell as a whole began as a symbiotic association between a proteobacterium and an achaeon and subsequently evolved a nucleus and endomembrane system thru the infolding 25.3 7 major branches of the eukaryotic tree ○ 1. Opisthokonts - animals and fungi ○ 2. Ameobozoans ○ 3. Archaeplastids ; plants ○ 4. SAR – stamenopiles, alveolates, rhizarians ○ 5. Cryptists  ○ 6. Haptists ○ 7. Excavates Protists: uniceulluar. Eukayroties that arent animals, plants or fungi but has a nucleus ○ Algae are photosyntheitc protists Opisthokonts: major group of organisms that includes animals, fungi and related protists Choanoflagellates: group of mostly unicellular protists is charaterized by a ring of microvilli, fingerlike projections that form a collar around the cell’s singel flagellum Microsporidia: parasites that live inside animal cells Ameobozoans: group of eukaryotes with amoeba-like cells that move and feed by extending cytoplasmic fingers called pseudopodia ○ Play an important role in soils ○ Some cause disease in humans Coenocytic: contaisn many nuclei within one giant cell Archaeplastids: superkingdom of land plants Molecular sequences for genes in red and green algae show the close evoltuonary relationship organelles to free-living cyanobacteria. Supports the hypothesis that eukaryotes initially gained the ability to photosyntheize thru their incorporation of symbiotic cyanobacterial cells Lecture 11: ❖ Protists likely evolved approx. 1.5-2 billion years ago Eukaryotes Paraphyletic ❖ Unlike prokaryotes, protists have: 1. A membrane-bound nucleus, with multiple, linear chromosomes 2. Cytoplasmic organelles including mitochondria and chloroplasts 3. Transcription and translation characteristics similar to other eukaryotes ❖ Photosynthesizing protists differ from plants and animals They can live as heterotrophs, no seed protection – plants No internal digestive tract, no complex development, no collagen – animals ❖ Protists are diverse Need water to move Kelps: largest, most complex protists ❖ Eukaryotes produce thru sexual reproduction, promoting genetic variation in two ways 1. Meiotic cell division results in gametes or spores that are genetically unique 2. In fertilization, new combinations of genes by the fusion of gametes ❖ Contracile vacuole: pumps water to prevent lysis (opening up) in freshwater ❖ Pellicle: layer of supportive protein fibers, gives structure ❖ Pseudopodia: lobes of cytoplasm for ameoboid movement Can be used for capturing prey ❖ Modes of locomotion: Ameboid motion via pseudopodia Swimming via flagella  Swimming via cilia ❖ Mitochondria are organelles that generate ATP Endosymbiosis theory: proposes that mitochondria originated when a bacterial cell took up residence inside a eukaryote about 2 billion years ago 1. Eukaryotic cell surrounds and engulfs bacterium 2. Bacterium lives within eukaryotic cell 3. Eukaryote supplies bacterium with protection. Bacterium supplies eukaryote with ATP Symbiosis: individuals of two different species live in physical contact Endisymbiosis: when an organism of one species lives inside an organism of another species ❖ Trypanosoma: causes sleeping sickness 19.2 Hierarchical: genes expressed at each stage in the process control the expression of genes that act later Drosophila development proceeds thru egg, larval and adult stages Fruit fly Drosophilia was used to understand the genetic control of its early development ○ Life cycle: 1. A fertifilized egg 2. Followed by a developing embryo 3. Larval stages 4. Pupa 5. Adult ○ DNA replication and nuclear divison begin soon after the egg and sperm nuclei fuse. Unlike mammals, the fruit fly’s embryo occur without cell division which results in the embryo is a single cell with many nuclei in its centre ○ Cellular blastoderm: the structure formed by nuclei in the single-cell embryo when they migrate to the periphery of the embryo and each nucleus becomes enclosed in its own cell membrane Gastrulation: cells of the blastoderm migrate inward, creating layers of cells within the embryo ○ Forms in three germ layers Ectoderm Mesoderm Endoderm Segmentation: formation of discrete repeating parts or segments in the developing body of many animals  ○ Three caephalic segments 1. C1-C3 (cephalic refers to the head) 2. T1-T3 (throax, middle region of an insect) 3. A1-A8 = 8 abdominal segements The egg is a highly polarized cell Christiane nusslein-volhard and Eric F. Wieschaus found that the development of Drosophilia fruit flies starts ecen before a dertifilzied egg is formed, in the maturation of the oocyte (unfertilifzed egg cell produced by the mother) ○ Also discovered mutant of the embryo’s developmental genes Nonmutant larvae: have anterior, middle and posterior segments Bicoid mutant larvae: lack anterior segments Nanos mutant larvae: lack posterior structures Maternal effect genes: gene expressed by the mother that affects the phenotype of the offspring Hunchback: targets genes of the embryo needed for the development of anterior structures such as the eyes, antennae Caudal: targets genes ofthe embryo needed for the development of posteriori structures such as genitalia Anterior-posterior gradient is set up by the maternal effect genes Thre classes of mutants: analysis showed that genes in the embryo controlling its development are turned on in groups ○ 1. Gap genes: leaves a gap pattern of segments Kruppel ○ 2. Pair-rule genes: encodes a set of transcription factors that help to regulate the next level in the segmentation hierarchy ○ 3. Segment- polarity genes: results in differentiation of the anterior and posterior regions of each segment Homeotic genes determine where different body parts develop in the organism Hox genes: control the pattern of expression of another set of genes ○ Specifies the identify of a body part or a segment during embryonic development Homeodomain: whose sequences are very similar from one homeotic protein to the next across different species Thalidomide: usined to treat morning sickness for pregnant women 18.3 DNA or proteins that are similar in sequence among distantly related organisms are evolutionarily conserved Animals have variety of different eyes ○ Arrangement of lenses allows a wide viewing angle and detection of rapid movement Pax6 is a master regulate of eye development Pax6 is important for eye development in fruit flies and mice Loss-of-function mutations: inactivates the normal function of a gene ○ Mutation that causes the green colour in Mdndel’s peas – mutant of an enzyme that that usually breaks down green pigment of chlorophyll Gain-of-function mutation: gene is expressed in the wrong place or time Cis-regulatory elements: help determine whether teh adjacent DNA is transcribed ○ Pax6 binds to these elements in many genes, causing soem genes to turn on and others off 19.2 Lytic pathway: a viral reproductive cyle that results in the destruction of the host cell. ○ Destroys host cell ○ Rapid and active, leading to cell lysis ○ Release of new viruses after lysis Lysogenic pathway: a viral reproductive cycle that inserts the viral genome into the host’s cell’s DNA ○ Host cell initially survives ○ Prophage: Bacterial virus that becomes integrated into the baterial DNA ○ Can sometimes lead to uncontrolled cell division Oncogene: a cancer-causing gene resulting from a mutation in proto-oncogene. Found in viruses. ○ Proto-oncogenes: cellular genes, play a role in normal cell division ○ Human proto-oncogenes can mutate into cancer-causing oncogenes 19.3 Viral infections trigger an immune response Pathogenicity: ability of an organism or virus to cause disease  Virulence: degree of severity the disease caused ○ Flu – usually described as mild, but it can become very severe and even lead to death in some individuals Epidemic: outbreak of an infectious disease that spreads rapidly and affects a large number of people in a particular region or community Pandemic: worldwide outbreak affecting many countries Primary response of the immune system involves the production of cytokines: ○ Cytokines – primary immune system: chemical messengers that activate other components of the immune system. Helps activate immune cells that help protect us from viruses ○ Memory cells – secondary immune response: they’re faster and stronger than the cytokines Influenza virus causes mild or severe disease Flu virus is spread thru sneezing, coughing and talking Flu is subject to evolution and can change quickly over time ○ Causes memory cells not to recognize the new forms of virus ○ Difficult to develop vaccines Hemagglutinin: a glycoprotein; binds to red blood cells which contain hemoglobin and causes these cells to agglutinate or clump together. ○ Controls viral entry into cells ○ Antigens: recognized by the immune system ○ Antigenic drift: gradual process by which mutation leads to changes in the amino acid sequences of antigens. Reason why a new flu vaccine is needed every year ○ Antigenic shift: reassortment of RNA strands in a viral genome, leading to sudden changes in cell-surface proteins HIV is a retrovirus that targets the immune system and causes AIDS Can be transmitted sexually between partners, from mother to fetus during pregnancy or birth HIV infects and kills specific cells of its host’s immune system People with HIV become have a weaker immune system, becoming more prone to cancer HIV gains entry into a T-cell by interacting with a CD4 receptor protein and a CCR5 co-receptor on the surface of T cells ○ CCR5: binds certain small secreted proteins that promote tissue inflammation in response to infection SARS-CoV-2 and other viruses cause emerging diseases Emerging diseases: infectious diseases that have appeared recently and/or spread rapidly ○ Ebola ○ Zika virus ○ SARS -CoV-2 Viruses that infect one species may evolve the ability to infect a new species ○ SARS-CoV-2 came from bats, but is unclear how it affected humans Lecture 12 ❖ Genes can turn on and off depending on during the embryonic phase Depends on where its located in the body ❖ Hox genes = homeo box Controls animal body plan Huge impact on expression of a thousand genes in their body ❖ Teratorgens: any agent that causes an abnormaily following fetal exposure during pregnnacy Acutane ❖ Stickleback variants: spines in dorsal and pelvic area ❖ Stickleback: variation in spines ❖ D, d, a, c, c, a, C b A C c T T T F t