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McMaster University
Jon Stone

Ch 1 - Biology and the Tree of Life 12/10/2012 11:01:00 AM CHAPTER 1 - BIOLOGY AND THE TREE OF LIFE Cell theory (all organisms are made of cells and that all cells come fro preexisting cells) natural selection (species change through time b/c individuals with certain heritable traits produce more offspring than others) Phylogenetic tree - graphical representation of the evolutionary relationships among species. Estimated by analyzing similarities and differences in traits Theory Is an explanation for a very general class of phenomena or observations Cell theory and theory of evolution focus on what organisms are made of and where they came from 1.1 - CELL THEORY Robert hooke used a crude microscope to examine the structure of a cork from an oak tree - saw cells Anton van Leeuwenhoek developed a much more powerful microscope and was the fist to view single-celled animalcules in pond water. Also human blood cells and sperm A cell is defined as a highly organized compartment that is bounded by a thin flexible structure called a plasma membrane and contains [ ] chemicals in a aq solution Where do cells come from? The first describes a pattern in the natural world and the 2nd identifies a process that is responsible for creating that pattern Spontaneous generation was a hypothesis Biologists use a theory to refer to proposed explanations for broad patterns in nature and hypothesis to refer to explanations for more tightly focused questions Prediction is something that can be measured and that must be correct if hypothesis is valid *louis pasteur - refer to experiment in text (pg 3) or slides - proved that cells arise only from preexisting cells and that the heat sterilization had not altered the capacity to support growth If all cells come from preexisting cells, it follows that all individuals in a pop of single celled organisms are related by common ancestry 1.2 - THE THEORY OF EVOLUTION BY NATURAL SELECTION Darwin and Wallace claimed that species are related by common ancestry and that the characteristics of species can be modified from generation to generation “descent with modification” Evolution - species are not independent and are related to one another Natural selection occurs whenever 2 conditions are met: individuals within a population vary in characteristics that are heritable and certain heritable traits help individuals survive better or reproduce more than do other versions Population is defined as a group of individuals of the same species living is the same area at the same time **natural selection acts on individuals but evolutionary change affects only populations **evolution occurs when heritable variation leads to differential success in reproduction Fitness - the ability of an individual to produce offspring. Higher fitness = more offspring Adaptation - a trait that increases the fitness of an individual in a particular environment Ex/ to create broccoli, horticulturists selected mustard species that were large and compact flowering stalks - over generations made broccoli 1.3 - THE TREE OF LIFE Speciation - where natural selection caused populations of one species to diverge and form a new species Speciation supports a clam that Darwin and Wallace made - that NS can lead to change b/w species as well as within Tree of life - a family tree of organisms Taxonomy - effort to name and classify organisms Carolus Linnaeus’s system: first part indicted the organism’s genus (closely related group of species) and the second identifies the organism’s species (made up of individuals that regularly breed together or have characteristics that are distinct from those of other species An organism’s genus and species designation is called its scientific name (always italicized). Genus names are capitalized Linnaeus said that diff types of organisms shouldnt be given the same genus and species names. Naming system is called binomial nomenclature Taxonomic levels: species, genus, family, order, class, phylum and kingdom For humans: homo sapiens, homo, hominidae, primates, mammalia, chordata, animalia Linnaeus proposed that species could be organized into 2 kingdoms - plants and animals. Organisms that do not move and produce their own food are plants XX Eukaryotes with a nucleus and prokaryotes are unicellular and w/o nucleus Now we have 5 kingdoms: monera (prokaryotes), protista (unicellular eurkaryotes), plantae, fungi, and animalia Carl Woese and colleagues’ goal was to understand phylogeny of all organisms - their actual genealogical relationships. They needed to study rRNA Woese: if the theory of evolution is correct then rRNA sequences should be very similar in closely related organisms but less similar in organisms that are less closely related Phylogenetic tree - a diagram that depicts evolutionary history. Branches are close to one another are closely related TREE OF LIFE SHOWED: Fundamental divisions in organism: the bacteria, Archaea and eukaryotes Woese created a new taxonomic level called domain. Some of the kingdoms that had been defined earlier do not reflect how evolution actually occurred Bacteria and archaea are much more diverse than anyone imagined 1.4 - DOING BIOLOGY Why do giraffes have long necks? FOOD COMPETITION: giraffes compete for food with other species of mammals. Giraffes with longer necks can reach food that is unavailable to other species. As a result, giraffes with longer necks survived overtime. However proved to be wrong because giraffes usually bend their necks to feed SEXUAL COMPETITION: females urinate into males’ mouth and they taste whether or not estrus has begun. Males then fight amongst themselves - swing their necks, harder blow, longer moment arm Experiments are a powerful scientific tool b/c they allow researchers to test the effect a single, well-defined factor on a particular phenomenon Y R CHILI PEPPERS HOT? Due to capsaicin. In humans capsaicin binds to heat sensitive cells in the tongue and mouth - sensation of burning. Josh tewksbury and gary nabhan proposed that the presence of capsaicin is an adaptation that protects chili fruits from being eaten by animals that destroy the seeds inside Null hypothesis - specifies that we should observe when the hypothesis being tested doesn’t hold **refer to diagram/experiment in text (pg15) or slides When doing experiments: include control groups (checks for factors other than the one being tests that might influence the experiment’s outcome) and conditions must be controlled (time, place etc) and repeating the test is essential Ch – 24 Evolution by Natural Selection 12/10/2012 11:01:00 AM CHAPTER 24: EVOLUTION BY NATURAL SELECTION Populations and species evolve meaning that their heritable characteristics change through time (changes in allele frequencies) NS occurs when individuals produce the most surviving offspring in a population Evolution by NS is not progressive and changes only the characteristics of the population. All adaptations are constrained by trade-offs and genetic/historical factors On the origin of species by means of natural selection - Darwin. Created a protest - they believed in special creation by god and darwin stated that life on earth was ancient and species change thru time 2 components of scientific theories: pattern and process. The pattern component is about facts (how things are in nature) and the process produces the pattern of observations. 24.1 - THE EVOLUTION OF EVOLUTIONARY THOUGHT A scientific revolution overturns an existing idea about how nature works and replaces it with another, radically different idea Plato claimed that every organism was created by God and were unchanging. Aristotle proposed that species were organized into a sequence based on increased size and complexity with humans at the top Typological thinking is based on the idea that species are unchanging types and that variations within species are unimportant or even misleading Lamarck was the first to propose the formal theory of evolution - change thru time Lamarck claimed that simple organisms originate at the base of the chain by spontaneous generation and then evolve by moving up in the chain over time. Also said that species change thru time via inheritance of acquired characters In contrast Darwin and Wallace proposed that evolution does not follow progressive patterns. The process responsible for change thru time is based on variation among individuals in populations Darwin claimed that instead of being unimportant or an illusion, variation among individuals in a population was they key to understanding the nature of species The theory of evolution by NS was revolutionary b/c it overturned the idea that species are static and unchanging and replaced typological thinking with population thinking. Also proposed a mechanism that could account for change thru time and be tested thru observation and experimentation Why darwin gets most of the credit? He developed he idea more thoroughly and provided massive evidence for it. He wrote a paper 17 years b4 writing his book but never published it out of fear. Wallace wrote a brief article of butterflies and NS and sent it to darwin and then bam! 24.2 - THE PATTERN OF EVOLUTION: HAVE SPECIES CHANGED THRU TIME? Descent with modification - all species today have descended from other and are modified and change thru time The pattern component of evolution by NS claims that species change overtime and are related by common ancestry Fossil - any trace of an organism that lived in the past. Fossil record consists of all the fossils that have been found and described in scientific literature Most fossils are found in sedimentary rocks Researchers began naming diff periods of geologic time, creating the sequence of eons, epochs and periods called geologic time scale. *radiometric dating Baron Georges Cuvier published an analysis of an extinct species then we accepted extinction as a reality. Recent analyses support the claim that more species have gone extinct than exist today. Continuously go extinct throughout Earth’s history Law of succession - fossils have resemblances to species today (same region) Transitional form - a fossil species with traits that are intermediate b/w those of older and younger species Oldest whale fossils are from fox-sized animals. Earliest whales were semi- aquatic animals and over 12 million years the limbs became more reduced and now strictly aquatic. Each of these transitional forms proves change thru time concept Vestigial traits - a reduced or incompletely developed structure that has no or reduced function but it is clearly similar to functioning structures in closely related species Pseudogenes - functionless DNA sequences Human coccyx = tail. Goose bumps. Ostriches have wings but dont fly etc Vestigial traits are evidence that the characteristics of species have changed overtime Current examples: bacteria have become resistant to drugs, insects to pesticides etc Darwin realized that species are related by common ancestry during a voyage on HMS beagle - galapagos islands (off ecuador). Studied mockingbirds - differences Mockingbird populations that colonized diff islands had changed thru time and formed new species Homology the study of likeness (similarities that exists in species) Genetic homology - a similarity in the DNA sequences of diff species Except for 1 or 2 codons in a handful os species, the same 64 mRNA codons specify the same amino acids in all organisms. All organisms today have a plasma membrane consisting of a phospholipid bilayer with interspersed proteins, transcribe the info coded in DNA to RNA via RNA polymerase, use ribosomes to synthesize proteins, employ ATP as energy and make copies of genomes via DNA polymerase Development homology - similarity in embryonic traits. Observed in morphology, or form of embryos. Also observed at the level of specific tissues Structural homology - similarities in adult morphology. Traits are similar in diff species b/c the species in question are related to each other by common descent. If species were created independently of one another, these types of similarities would not occur Darwin argued that the pattern called evolution was much more consistent with the data than was the pattern predicted by special creation. Descent with modification was a more successful and powerful scientific theory b/c it explained observations such as vestigial traits and the close relationships among species on neighbouring islands - that special creation could not EVIDENCE FOR EVOLUTION: Species are not static but change thru time: most species have gone extinct, fossil species resemble living species, transitional forms document change thru time, earth is ancient, vestigial traits are common, populations can be observed changing today Species are related, not independent: closely related species live in the same area, homologous traits are common (genetic, development and structural) 24.3 - THE PROCESS OF EVOLUTION: HOW DOES NS WORK? Darwin broke the process of evolution by NS into steps in a logical sequence: The individual organisms that make up a population vary in traits they possess, such as their size and shape Some of the trait diff are heritable In each generation many more offspring are produced than can possibly survive. Only some will survive long enuff to produce offspring The subset of individuals that survive best and produce the most offspring is not a random sample of the population. Individuals with certain heritable traits are more likely to survive and reproduce. NS occurs when individuals with certain characteristics produce more offspring than do individuals without Today evolution by NS occurs when heritable variations leads to differential success in survival and reproduction Evolution is defined as a change in allele frequencies in a population overtime Darwinian fitness - ability of an individual to produce offspring, relative to that ability in order individuals in the population 24.4 - EVOLUTION IN ACTION: RECENT RESEARCH ON NS Mycobacterium tuberculosis (causes TB) declined in countries where living conditions were acceptable. Antibiotic = rifampin. However infection surged as the bacteria became resistant to the antibiotic. Guy had TB, gave him antibiotics, got better, then readmitted, then antibiotics again but died. Biologists examined the DNA before and after and saw a point mutation in a gene called rpoB (codes a part of RNA polymerase - transcribes DNA to mRNA) the mutation changed cytosine to thymine. Substitution of leucine for a serine prevents rifampin from binding efficiently Darwin’s 4 postulates: Did variation exist? Due to mutation, both resistant and nonresistant strains of TB were present prior to administration of the drug Heritable? The variation in the phenotypes was due to variation in genotypes Variation in reproductive success? Only a tiny fraction of M. Tuberculosis cells in the patient survived the first round of antibiotics long enuff to reproduce Selection occur? Cells with drug resistant allele had higher reproductive success when rifampin was present than did cells with normal allele Individual cells did not evolve. When NS occurred individual cells just survived or died. Only populations evolve - allele frequencies change in populations Peter and Rosemary Grant investigated changes in beak size, shape and body size in finches in galapagos islands Natural experiments allow researchers to compare treatment groups created by an unplanned, natural change in conditions. After drought the finches had deeper beaks - able to break thru tough fruit. When a lot of rain fell, smaller finches had a higher reproductive rate. Continued evolution = continued changes in environment. Lower bmp4 = shallow beak and higher bmp4 = deeper beak 24.5 - THE NATURE OF NS AND ADAPTATION NS appears to be simple but appearances can be deceiving. Selection acts on individuals but evolutionary change occurs in populations Lamarck said individuals change in response to changes posed by the enviro and then the changed traits are passed on. Darwin said individuals do not change when they are selected - just produce more offspring than others. Tricky - ex when frogs are exposed to extremely cold temps, their bodies produce a natural antifreeze - molecules that protect their tissues Acclimation - changes in an individual’s phenotype that occur in response to changes in environmental conditions **adaptations do not occur b/c organisms want or need them. Under evolution by NS there is no such thing as a higher or lower organism. Evolution by NS is not progressive - favours individuals that happen to be better adapted to the enviro at that particular time Individuals with self-sacrificing alleles die and do not produce offspring. But individuals with selfish, cheater alleles survive and produce offspring. As a result, selfish alleles increase in frequency while self-sacrificing alleles die out. This it is not possible for individuals to sacrifice themselves for the good of the species Best example of nonadaptive traits involves evolutionary changes in DNA sequences Genetic correlation - constraint, occurs b/c of pleiotropy. Lack of genetic variation is also important on adaptation Fitness trade-off - compromise b/w traits in terms of how those traits perform in the environment. Ex finches with larges beaks could get food however they need a lot because they were bigger B/c selection acts on many traits at once, every adaptation is a compromise All traits have evolved from previously existing traits Ch – 25 Evolutionary Processes 12/10/2012 11:01:00 AM CHAPTER 25 - EVOLUTIONARY PROCESSES Hardy-weinberg principles acts as a null hypothesis when researchers want to test whether evolution or nonrandom mating is occurring at a particular gene NS produces adaptation, genetic drift causes random fluctuations in allele frequencies, gene flow equalizes allele frequencies b/w pop, mutation introduces new alleles Inbreeding changes genotype frequencies but does not change allele frequencies Sexual selection leads to evolution of traits that help individuals attract mates 25.1 - ANALYZING CHANGE IN ALLELE FREQUENCIES: HARDY- WEINBERG Hardy and weinberg analyzed what happens to frequencies of alleles when many individuals in a population mate and produce offspring. They imagined that all of the gametes produced in each generation go into a single group called gene pool and then combine at random to produce offspring To determine which genotypes would be present in the next generation and in what frequency HW had to calculate what happened when 2 gametes were plucked at random and each pair was combined to form offspring P^2 + 2pq + q^2 = 1. Homo dominant, hetero, homo recessive 5 conditions must be met in order for HW: no NS, no genetic drift or random allele frequency changes, no gene flow, no mutation, random mating HW principle functions as a null hypothesis. Given a set of allele frequencies, it predicts what genotype frequencies will be when NS, mutation, genetic drift and gene flow are not affecting the gene; and when mating is random. If biologists observe genotype frequencies that do not conform to HW it means that something interesting is going on - nonrandom mating or allele frequencies are changing for some reason ** refer to MN blood groups and HLA gene examples in slides 25.2 - TYPES OF NATURAL SELECTION Balancing selection/ heterozygote advantage - hetero have higher fitness than homo. Consequence is that genetic variation is maintained in populations Genetic variation - refers to the # and relative frequency of alleles that are present in a particular population If genetic variation is low and the enviro changes population may face extinction Directional selection - avg phenotype of pop changed in 1 direction. DS tends to reduce the genetic diversity of populations. If it continues overtime the favoured alleles will reach a frequency of 1 while disadvantageous alleles will reach a frequency of 0. Purifying selection - when disadvantageous alleles decline in frequency Stabilizing selection - reduce both extremes in a population. 2 important consequences: no change in the avg value of a trait overtime and genetic variation in the pop is reduced Disruptive selection - eliminated phenotypes near the avg value and favours extreme phenotypes. Overall amount of genetic variation is maintained. *important b/c it sometimes plays a part in speciation (formation of new species) 25.3 - GENETIC DRIFT Genetic drift is undirected. Defined as any change in allele frequencies in a pop that is due to chance. Allele frequencies change due to blind luck - aka sampling error GD is random with respect to fitness. The allele frequency changes are not adaptive GD is most pronounced in small pop. Smaller the pop = higher sampling error Overtime GD can lead to the random loss or fixation of alleles Genetic marker - a specific allele that causes a distinctive phenotype GD decreased genetic variation within pop and increased genetic diff b/w pop Founder effect - change in allele frequencies that occur when a new pop is established If a large population experiences a sudden reduction in size, a pop bottleneck is said to occur (disease outbreaks, natural catastrophes etc) Genetic bottleneck - sudden reduction in # of alleles in a population Drift violates the assumptions of the HW principle 25.4 - GENE FLOW Gene flow - movement of alleles from one pop to another. Has one outcome: equalizes allele frequencies b/w the source pop and the recipient pop Gene flow homogenizes allele frequencies among populations *refer to slides for examples Gene flow is random with respect to fitness - the arrival or departure of alleles can increase or decrease average fitness, depending on the situation. But a movement of alleles b/w populations tends to reduce genetic differences b/w them 25.5 MUTATION Occur when DNA polymerase makes an error as it copies a DNA molecule, resulting in a change in the sequence of deoxyribonucleotides It is an evolutionary mechanism that increases genetic diversity in populations Mutation is random with respect to the fitness of the affected allele Most mutations in sequences that code for a functional protein or RNA result in deleterious alleles (lower fitness) can be beneficial also As an evolutionary mechanism, mutation is relatively slow compared with selection, genetic drift, and gene flow Mutation introduces new alleles into every individual in every pop in every generation. If mutation did not occur, evolution would eventually stop. W/o mutation there is no variation for NS to act on **Table 24.5 on page 542 25.6 - NONRANDOM MATING Inbreeding - breeding b/w relations - share common ancestor. It increases homozygosity. It does not cause evolution b/c allele frequencies do not change in the population as a whole. Inbreeding changes genotype frequencies not allele (self-fertilization is most common) Inbreeding depression is a decline in avg. Fitness that takes place when homo increases and hetero decreases. Results from 2 processes: Many recessive alleles represent loss-of-function mutations (exist in hetero usually) inbreeding increases the frequency of homo recessive and loss-of- function mutations are usually deleterious or even lethal for it Many genes (esp. Fighting disease ones) are under intense selection for hetero. If an individual is homo at these genes, then fitness declines offspring of inbred matings are expected to have lower fitness than the progeny of outcrossed matings. Therefore no marriages b/w family members in humans Inbreeding does not cause evolution directly it can speed the rate of evolutionary change. Increases the rate at which purifying selection eliminates deleterious recessive alleles from a population Kermode bear - white fur. Sexual selection - when individuals within a pop differ in their ability to attract mates. Favours individuals with heritable traits that enhance ability to obtain mates Bateman-trivers theory contains 2 elements: a claim about the pattern in the natural world and a mechanism hat causes the pattern Sexual selection acts more strongly on males than females. Eggs are $ but sperm is cheap. Therefore females invest much more in their offspring than do males Fundamental asymmetry of sex has 2 consequences: B/c eggs are large and $ females produce few young over a lifetime. Her fitness is limited by her ability to gain the resources to produce more eggs and healthier young Sperm is simple to produce that a male can father many offspring. Fitness is limited by the number of females they can mate with ** if females invest a lot in offspring then they should protect that investment by being choosy about their mates. If males invest little in each offspring they should be willing to mate with any female. If there are equal number of males and females in the pop, then males have to compete with each other - therefore sexual selection acts more strongly on males In birds females mate with males that are well fed and in good health. 3 observations: colourful feathers/beak is due to carotenoids, carotenoids protect tissues and stimulate immune systems to fight disease more effectively, animals cant synthesize their own carotenoid but plants can In many species females prefer to mate with males that care for young or that provide the resources required to produce eggs (female kiwis and large eggs twice their size) Territory is an area that is actively defended and that provides exclusive use Males battle with other males and females cant choose - just go with the winner. Elephant seals for ex - larger body mass = better chance of winning = + kids Sexual dimorphism - traits that differs b/w males and females. Range from weapons (horns etc) to behaviour. Humans are dimorphic in size, body hair etc Ch 26 Speciation 12/10/2012 11:01:00 AM CHAPTER 26 - SPECIATION Occurs when pop of the same species become genetically isolated by lack of gene flow and then diverge from each other due to selection, GD, mutation Pop can be recognized as distinct if they are isolated, distinct morphological traits or form independent branches on a phylogenetic tree Pop can be genetically isolated if occupy diff geographic areas When pop come back into contact they may fuse, diverge, stay partially differentiated or have offspring that form a new species When gene flow ends, allele frequencies are free to diverge Isolation occurs from lack of gene flow and divergence occurs b/c selection, GD and mutation proceed independently 26.1 HOW ARE SPECIES DEFINED AND IDENTIFIED If gene flow stops, then mutation, selection and drift act independently. If a new mutation creates an allele that changes the phenotype of individuals in one pop, there is no longer any way for that allele to appear in the other pop. Allele frequencies and other characteristics in the pop diverge - become distinct species overtime Species - an evolutionarily independent pop or group of pop. 3 criteria for identifying species: biological species concept, morphospecies concept, phylogenetic species Biological species concept - identify species by reproductive isolation (no gene flow) pop dont interbreed = distinct species Prezygotic isolation prevents individuals from diff species from mating Postzygotic isolation offspring of matings b/w members of diff species do not survive or reproduce (hybrid) Biological concept has disadvantages - reproductive isolation cannot be evaluated in fossils or in species that produce asexually. Difficult to apply when closely related pop dont overlap with each other geographically Morphospecies concept distinguishes features that are most likely to arise if pop are independent and isolated from gene flow. Useful when biologists have no data on the extent of gene flow. Disadvantage is that features used to distinguish species are subjective Phylogenetic species concept based on reconstructing the evolutionary history of populations (applicable and precise) Monophyletic group (clade or lineage) consists of ancestral pop, all of its descendants and only those descendants On a tree of pop, each tip is a phylogenetic species Phylogenetic concept has 2 distinct advantages: applied to any pop and it is logical b/c pop are distinct enough to be monophyletic only if they are isolated from gene flow and have evolved independently. Disadvantage - carefully estimated phylogenies are available only for a tiny subset of pops on the tree of life READING a phylogenetic tree: branches represent pop thru time. Nodes occur when ancestral group splits. If more than 2 descendant groups emerge from a node the node is called a polytomy. Tips are the tree’s endpoints which represent groups living today or a dead end. Most basal (at the bottom) node on the tree = most ancient. Rotate nodes 180 = equivalent. Read roots to tips Subspecies are populations that live in discrete geographic areas and have distinguished features, such as colouration or calls (but arent distinct enough) Dusky seaside sparrow was in trouble, taken in and bred with females from a nearby species, plan backfired b/c they mixed atlantic coast and gulf coast (not preserving genetic diversity) dusky seaside lost forever 26.2 - ISOLATION AND DIVERGENCE IN ALLOPATRY Genetic isolation happens when pops become physically separated. Physical isolation occurs in 2 ways: dispersal or vicariance Vicariance a physical splitting of habitat Speciation that begins with physical isolation via dispersal or vicariance is known as allopatric speciation Pops that live in diff areas are said to be allopatry Biogeography - study of how species and pops are distributed geographically Colonization trigger speciation for 2 reasons: the physical separation b/w pops reduces or eliminates gene flow and GD will cause the old and new pops to diverge Characteristics of a colonizing pop are likely to be diff from the characteristics of the source pop due to fonder effects. Subsequent NS may extend the rapid divergence that begins with GD Vicariance events during the most recent ice age are thought to be responsible for the origin of many species today Gondwana - supercontinent. Ratites diverged and changed accordingly 26.3 - ISOLATION AND DIVERGENCE IN SYMPATRY Sympatry when pops live in the same geographical area to make interbreeding possible Sympatric speciation - occurs even though gene flow is possible - is rare or nonexistent Even tho sympatric pops are not physically isolated, they may be isolated by preferences for diff habitats Mutation reduces gene flow b/w mutant and normal individuals - mutant individuals have more than 2 sets of chromosomes - polyploidy Polyploidy occurs when an error in meiosis or mitosis results in a doubling of the chromosome number Tetraploid and diploid individuals rarely produce fertile offspring when they mate - their pops are reproductively isolated Autopolyploid - individuals are produced when a mutation results in a doubling of chromosome number and the chromosomes all come from the same species (maidenhair fern became tetraploid due to an error in meiosis) Allopolyploid - individuals are created when parents that belong to diff species mate and produce an offspring where chromosome number doubles (tragopogan hybridized and formed offspring that became tetraploid and formed new species) 26.4 - WHAT HAPPENS WHEN ISOLATED POPULATIONS COME INTO CONTACT? Prezygotic isolation - mating b/w pop is rare, gene flow is minimal and diverge Reinforcement - NS for traits that isolate populations. Selected traits reinforce diff that developed while pops were isolated from each other. If 2 pops diverged and are distinct genetically their hybrid offspring will have lower fitness that parents. If closely related species are sympatric (same area) they seldom mate with each other (allopatric!!) Hybrid zones - geographical area where interbreeding occurs and hybrid offspring are common. Depending on fitness of hybrid offspring and extent of breeding hybrid zones can be narrow, wide, short or long lived. (townsend’s warblers and hermit warblers) hybridization = creation of new species New species thru hybridization - hybrid offspring created a third, new species that had unique combinations of alleles from each parental species and diff characteristics Outcomes of secondary contact: fusion, reinforcement, hybrid zone, extinction, new Ch 27 – Phylogenies and History of Life 12/10/2012 11:01:00 AM CHAPTER 27 - PHYLOGENIES AND THE HISTORY OF LIFE Phylogenies and fossil record are the major tools that biologists use to study the history of life Cambrian explosion was the rapid morphological and ecological diversification of animals that occurred Adaptive radiations are a major pattern in the history of life. They are instances of rapid diversification associated with new ecological opportunities and new morphological innovations Mass extinctions have occurred thruout history - eliminate most of the species 27.1 - TOOLS FOR STUDYING HISTORY: PHYLOGENETIC TREES Phylogeny - the evolutionary history of a group of organisms Phylogenetic tree - shows ancestor descendant relationships among pops/species. The branch represents a pop thru time, where branch diverges = node Phylogenetic trees are effective of summarizing data on evolutionary history (estimate) Phenetic approach - based on computing a stat that summarizes the overall similarity among pops based on that data (ex genetic distance - dna) Cladistic approach - based on the realization that relationships among species can be reconstructed by identifying shared derived characters or synapomorphies A synapomorphy is a trait that certain groups of organisms have that exists in no others. Allows biologists to recognize monophyletic groups (clades/lineages) Homology occurs when traits are similar due to shared ancestry. Homoplasy occurs when traits are similar for reasons other than common ancestry Convergent evolution occurs when NS favours similar solutions to the problems posed by a similar way of making a living-dont occur in the common ancestor of similar species (common cause of homoplasy) If similar traits found in distantly related lineages are similar due to common ancestry, then similar traits should be found in many intervening lineages on the tree of life Parismony the most likely explanation or pattern is the one that implies the least amount of change Convergent evolution and other causes of homoplasy should be rare compared with similarity due to shared descent, so the tree that implies the fewest overall evolutionary changes should be the one that most accurately reflects what really happened during evolution SINEs - short interspersed nuclear elements are transposable elements (whales and hippos) 27.2 TOOLS FOR STUDYING HISTORY: THE FOSSIL RECORD Only the fossil record provides direct evidence about what organisms lived in the past looked like where they lived and when they existed Fossil - piece of physical evidence frm an organism that lived in the past Fossil record the total collection of fossils How fossils form? Ex tree falls, flooding brings in sand and mud, over the years filled with sediment - occurs when remains are buried in sediments 4 types: intact (no decomposition), compression, cast, permineralized Limitations: Habitat bias - organisms that live in areas where sediments are actively being deposited are much more likely to form fossils Taxonomic bias - clams, snails etc with hard parts have higher tendency (fossils) Temporal bias - earth’s plated go on top of each other - older = demolished Abundance bias - abundant leaves more evidence Precambrian is split into hadean, archaean, proterozoic eons. Important things to note: life was unicellular and O2 was absent from oceans and atmosphere (542 mya) Phanerozoic eon - 542 mya and present 3 divisions Paleozoic - saw the origin and initial diversification of animals, lands, plants, and fungi - land animals Mesozoic - age of the reptile. Gymnosperms were dominant plants and dinosaurs Cenozoic - age of mammals. Angiosperms were dominant plants and mammals Molecular clock - analyzing silent mutations and other changes in dna that do not affect gene function. Changes are affected by increase to fixation by GD not NS. Drift fixes mutations at a steady rate. Mtdna = mitochondrial dna (maternal) 27.3 - THE CAMBRIAN EXPLOSION First animals appeared - burst of diversification (recall all life was unicellular for 3byrs) First animals - sponges jellyfish, then 50my later every major group of animals emerged with shells, exoskeletons, eyes, tails head etc - spectacular period Cambrian explosion is documented by 3 major fossil assemblages that record the stae of animal life: doushantuo fossil (microscopic), ediacaran fossils (small, soft-bodied), burgess shale fossils (diverse large animals with hard parts Doushantuo microfossils - sponges and posssibly other tiny creatures that made their living by filtering organic debris from the water The ediacaran faunas - these animals were small individuals that burrowed in sediments, sat immobile on the sea floor or floated in the water Burgess shale faunas - filled with animals that had eyes, mouths, limbs and shells. They swam, burrowed, walked, ran, slithered clung or floated. There were predators, scavengers etc. Diversification Was the increase in morphological complexity during the Cambrian possible b/c of an increase in the number and complexity of homeotic genes? Look for correlations b/w the evolutionary history of animal lineages, genetic makeup and morphology Logic behind new genes new bodies was that gene duplication could have occurred before and during the cambrian explosion and produced new copies of homeotic genes. These new genes would make possible the new body plans and appendages recorded in the burgess shale fauna Duplication of hox genes has been important in making he elaboration of animal body plans possible. Changes in the expression and function of existing genes have been equally important 27.4 - ADAPTIVE RADIATIONS Adaptive radiation occurs when a single lineage produces many descendant species that live in a wide diversity of habitats and find food in a variety of ways. The hallmark of an adaptive radiation is rapid speciation and ecological diversification within a single lineage When adaptive radiation is analyzed the common theme is ecological opportunity - often occurs when habitats are unoccupied by competitors Another trigger is morphological innovation (wings, flowers’ reproductive structures, cichlids (jaws in throat) feathers and wings etc) 27.5 MASS EXTINCTIONS Mass extinction refers to the rapid extinction of a large number of lineages scattered throughout the tree of life Background extinction refers to the lower avg rate of extinction observed when a mass extinction is not occurring Background = when normal enviro change, diseases, competition. Mass = temporal change. Mass like GD and background are NS Extinction of dinosaurs = asteroid struck earth. Proof = iridium is an abundant component of asteroids. Shocked quartz and microtektites . One hypothesis - animals that are capable of inactivity survived this catastrophe Ch 51 – Population Ecology 12/10/2012 11:01:00 AM Chapter 51 – Behaviour Behavior is the response to a stimulus Proximate or mechanistic, causation explains how actions occur in terms of neurological, hormonal and skeletal-muscular mechanisms involved. Ultimate or evolutionary causation explains why actions occur based on their evolutionary consequences and history. Leading hypothesis to explain homing behavior is that the ability to navigate allows spiny lobsters to search for food over a wide area under cover of darkness then return to a safe refuge before sharks and other large predators that hunt by sight can find them Redback spider – female eats males b/c males sacrifice themselves to increase his reproductive success 51.1 types of behavior: an overview Learning is defined as a change in behavrious that results from a specific experience in the life of an individual (check graph p1207) Highly inflexible behavior patterns are called fixed action patterns of FAPs. FAPs are stereotyped and are triggered by stimuli called releasers or sign stimuli. FAPS are examples of what biologists call innate behavior Common to observe innate behavior in response to situations that have high impact on fitness and demand a reflex-like, unlearned response, or situations where learning is not possible Animals make choices – take in info and decide what to do. Take in costs and benefits – terms of ability to produce offspring Optimal foraging – animals should maximize their feeding efficiency. Occurs? Studied white-fronted bee-eater. Mated pairs of this species dig tunnels in riverbanks and raise their young inside. Form colonies and each pair has to look for food. Foraging behavior depends on distance travelled Female barn swallows choose mates with longer tails b/c they are more efficient in flight and more successful in finding food Experiment: short tail, outermost tail feathers cut and glued back, no change, and elongated tails. Elongated tails mated sooner and raise more offspring Bluehead wrasses: a large male fertilizes all eggs in territory. When he dies the largest female changes sex and takes his place. Consider for example a large female produce 20 eggs per year. By changing sex she can produce 20-80 51.2 – learning Classical conditioning – trained by experience to give the same response to more than 1 stimulus Imprinting – ducklings adopt as their mother the first moving thing they see. Why? Preyed by foxes etc easily so as soon as they hatch they have to recognize a moving object and follow it to increase the fitness of offpring. Happens during critical period. Key aspects: fast and irreversible In young chickens song learning is innate. In contrast, white crowned sparrows do not sing a normal song unless they hear it Cognition: recognition and manipulation of facts about the world, combined with the ability to form concepts and gain insights. Cant be observed directly. Must design experimental situations that require animals to manipulate facts or info and demonstrate an ability to form novel associations or insights New Caledonian crows: use sticks, and complex leaves as hooks and spearing tools – support hypothesis that crows think. Experiment: food placed in a bucket and had to retrieve it with straight or hooked wires. Mostly females bent the straight wires Biologists view learning as an adaptation that allows individuals to change their behavior in response to a changing and unpredictable enviro. Type of learning is correlated with type of enviro unpredicitability it encounters Norway rats – extremely adept at learning to navigate mazes, and avoid poisonous foods. Scrub jays remember where they stored seeds 51.3 – how animals act: hormonal and neural control When behavior is flexible and condition dependent, it means that an individual has the potential to behave in a variety of ways. Anolis carolinensis – lizard. Testosterone in males and estradiol in females are responsible for seasonal changes in behavior. Critical for them to start their sexual activity at the same time. Experiment: 5 treatment groups – same physical enviro. Each was given identical food. Biologists exposed the groups to artificial lighting that simulated long days and short night of spring. 1)single isolated females 2)groups of females 3)pairs of lizards 4)single females with castrated males 5)single females with breeding males. Conclusion: females need to experience springlike light and temp and exposure to breeding males Echolocation – emit high pitched pulses of sound and listen for echo. When moths hear a bat is close it makes a power dive and drops like a stone. Moths have ears and when membrane vibrates in response to bat sounds, the sensory neurons generate action potentials. The brain responds by shutting down neurons that control flight muscles (hypothesis) 51.4 – communication Communication – any process in which a signal from one individual modifies the behavior of a recipient individual A signal is any information-containing behavior For communication to occur a signal must be sent and acted on! Can be acoustic, visual, tactile, olfactory (scent marking) Type of signal correlates with habitat. Ex in water light is dispelled but sound is not – humback whale songs to communicate Animals that are active during the day rely on visual communication and at night communicate via sound or cents. Can be used in conjunction(red winged black birds) Disadvantages: acoustic can attract predators  Honeybee dance = orientation of the waggle part of the dance varied and that the variation correlated with the direction of the food source from the hive. Food placed directly away from the sun – waggle dance directly downward. 90 degrees to the right of the sun bees would waggle 90 degrees to the right of vertical  Round dance is used to indicate the presence of food within 80 to 100 m of the hive. Waggle dance is used to indicate direction and distance to food that is over 100 m from the hive  Natural selection has favoured the evolution of the deceitful communication  Anglerfish has an appendage that dangles near its mouth. If another fish approaches it the anglerfish attack  Male and female fireflies flash a species specific signal to each other during courtship. Predatory photuris fireflies can mimic the pattern – female attracts a male and then eats him  Butterfly looks toxic  Individuals increase their fitness by providing inaccurate or misleading info to members of a diff species  When mantis shrimps moult, they lack any external covering and cannot use their claws – unable to defend cavities where they live  Mating system of bluegill sunfish – male sets up territories. Some males mimic the look of females. When females lay eggs mimic releases sperm and then goes away. Female-mimic male fathers offspring but does not help care for them  Lying works only when it is relatively rare. If deceit becomes common, then NS will favour inidividuals that can detect and avoid liars. But if liars are rare then NS will favour individuals that are occasionally fooled but are more commonly rewarded by responding to signals in a normal way 51.5 – MIGRATION AND NAVIGATION  Orientation – a movement that results in a change of position. Simplest form is called taxis (positioning the body toward of away from a stimulus)  Moth attracted to light = phototaxis. Phonotaxis – sound  Migration – long distance movement of a pop associated with a change of seasons  Arctic terns nest along atlantic coast, fly south and chicks make the return trip on their own  Individuals that migrate achieve higher reproductive success than do individuals that don’t  Monarch butterflies migrate to wintering areas and new breeding areas instead of overwinter in northern north America  Salmon eggs and young are safer and thrive better in freshwater habitats than they do in the ocean  3 categories of navigation: piloting (familiar landmarks), compass orientation (specific direction), true navigation (locate a specific place on earth’s surface)  piloting: offspring follow parents and memorize the route. Homing pigeons can find their way home even when they are released anywhere. They use piloting to navigate the final stages of a journey home  compass orientation: based on sun and stars. Rises in the east, due south at noon an sets in the west. Circadian clock maintains a 24hr rhythm of chemical activity. Clock is set by light-dark transitions of day and night.  ^simpler on clear nights – use north star. Hypothesis – birds can detect magnetism by their visual system through an unknown molecular mechanism. Or: have small particles of magnetic iron (magnetite in their bodies)  birds have multiple mechanisms of finding a compass direction 51.6 THE EVOLUTION OF SELF-SACRIFICING BEHAVIOUR  altruism is behaviour that has a fitness cost to the individual exhibiting the behaviour and a fitness benefit to the recipient of the behaviour – aka self sacrificing behaviour  ^decreases individual’s ability to produce offspring but helps others produce more offspring  black tailed prairie dogs: alarm calling. When a predator approaches they give alarm calls that alert others to run. Risky because they draw attention to themselves.  Br > C where b is the fitness benefit to the recipient, r is the coefficient of relatedness and c is the fitness cost  Coefficient of relatedness: measure of how closely they are related  Hamilton’s rule: important bc it shows that individuals can pass their alleles on to the next generation not only by having their own offspring but also by helping close relatives produce more offspring  If the fitness benefits of altruistic behaviour are high for the recipients and cost is low then alleles associated with that behaviour will be favoured by NS  Close relatives are very likely to have copies of the altruistic allele and help from close relatives allow more production o
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