Evolution Notes - PDF

EVOLUTION 1  OVERVIEW  Theory of evolution: proposed by Darwin. All living organisms are descended from a common ancestor. Change of a species over time.  Horizontal gene transfer: genes can be transferred from 1 cell to another within the same generation...

EVOLUTION 1  OVERVIEW  Theory of evolution: proposed by Darwin. All living organisms are descended from a common ancestor. Change of a species over time.  Horizontal gene transfer: genes can be transferred from 1 cell to another within the same generation (Ex: plasmids between bacteria).  Many species will become extinct before they are classified and studied.  Variations in individuals within a population occur through mutation, allowing desirable traits to be passed to the next generation. Also sexual reproduction, Recombination and Random Assortment of Tetrads.  Due to competition and other envr. pressures, individuals that have more adaptive characteristics are more likely to survive and reproduce, passing those traits to the next generation with increased frequency. 2  OVERVIEW 2  When environments change, unfavorable traits may become favorable and vice versa.  Organisms may evolve through an accumulation of favorable traits in succeeding generations.  Natural selection explains the unity and diversity of life.  Divergent evolution: 2 species evolve in different directions from a common point.  Convergent evolution: similar traits with same function evolve in multiple species exposed to similar selection pressure.  Evolution continues to occur, but might be “slow” for some species. 3  INTRO  Linnaeus classification system attempted to organize all living things into schemes that demonstrated an increasing complexity of life.  Cuvier found fossilized remains of organisms changed as he dug deeper into rock layers, indicating organisms present in area had changed over time.  Darwin observed finches (birds) in the island chains of the Galapagos that were similar, but had distinct differences. They closely resembled one present on the mainland so he initially thought they were modified  Varied beaks helped the birds acquire specific type of food. 4  LEVELS OF CLASSIFICATION  Taxonomy: science of classifying organisms to construct inclusive groupings.  Hierarchical system: organization from largest to smaller categories.  Linnaeus classification system for a dog  LUCA (Last Universal Common Ancestor)  Domain: Bacteria, Archaea, Eukarya  Kingdom: Animalia, Plantae, Fungi, Protista  Phylum: Chordata  Class: Mammalia  Order: Carnivora  Family: Canidae  Genus: Canis  Species: Canis lupus 5  BINOMIAL NOMENCLATURE  Each name is capitalized except for species  Genus and species names are italicized  Binomial nomenclature: 2 name system comprised of genus and species to make an organism’s scientific name.  Taxon: name at each classification level  Subspecies: members of the same species that are capable of mating and reproducing viable offspring, but consider separate subspecies due to geographic or behavioral isolation.  At each sublevel the organisms become more similar bc they are more closely related  Scientists used to classify organisms based on physical characteristics (morphology), but with tech advances DNA is used to build more precise phylogenies. 6  PHYLOGENY TREES  Phylogeny tree: tool used to how evolutionary pathways and connections among organisms. Consider hypothetic. It is not taxonomic classification diagram.  Rooted trees: contain a single lineage at base representing comm. ancestor 7  NATURAL SELECTION  Natural selection: “survival of the fittest” represents more prolific reproduction of individuals with favorable traits that survive envr. change because of those traits, which lead to evolutionary change.  1: most characteristics of organisms are inherited: passed down from parent to offspring.  2: more offspring are produced than are able to survive. Resources for survival & reproduction are limited leading to competition.  3: Offspring vary among each other in regard to their characteristics and variations inherited. 8  NATURAL SELECTION  Most successful variants will outcompete the rest for limited resources resulting in those traits better represented in next generation, which leads to changes in populations over generations: descent with modification.  Ultimately, there is greater adaptation of population to local environment. Only mechanism of adaptive evolution.  Darwin & Wallace separately presented idea of natural selection in 1858 (before Mendel). Origin of Species outlined in considerable detail arguments for evolution by natural selection.  Demonstrations of evolution by natural selection are time consuming and difficult to obtain. (Why?) 9  VARIATION  Variation: genetic (why?) differences among individuals in a population.  Development: changes that happen during lifetime. Not heritable.  Natural selection can only take place if there is variation.  Mutation: change in DNA, ultimate source of new alleles.  A change in phenotype may (why?) result in decreased or increased fitness which leads to lower likelihood of survival or fewer offspring or vice versa.  Sexual reproduction also leads to genetic diversity producing unique combinations of alleles (Hybrids).  Recombination/Crossover & Random Arrangement of Tetrads 10  MUTATION Mutation: changes to an organism’s DNA. They drive diversity in populations. Species evolve because of accumulations of mutations that can occur over time. Most common way to introduce new genotype and phenotype variety. Harmful mutations are quickly removed by natural selection Beneficial can spread throughout population Beneficial is defined by whether it helps an organism survive or/and reproduce Some are unaffected by natural selection (neutral) 11  ADAPTATION  Adaptation: heritable trait that helps survival and reproduction of organism in its present environment. Cannot change over lifetime. Born with it.  Adaptation allows organism increase chances of survival  Which grants increase chances of mating Which grants increase chances of producing an offspring Which grants increase chances of passing on genetic information  Population is considered adapted when change in range of genetic variation occurs over time that increases its fitness.  Fit: organism equipped to have higher chances of surviving in their current envr  Whether or not trait is favorable depends on environmental conditions at the time. Same trait is not always selected because environment can change. 12  FITNESS Natural selection only acts on population’s heritable traits as those are the only ones passed down to the next generation. Adaptive evolution: increase in frequency of beneficial alleles and decrease in deleterious alleles due to selection. Natural selection acts at the level of individual Evolutionary fitness: an individual’s ability to survive and reproduce (Darwinian) Relative fitness: individual’s ability to survive and reproduce compared to rest of population Directly ties with which individual are contributing more offspring for next generation and how the population may evolve. Natural selection influences the allele frequencies in a population 13  TIME  Physical changes occur over large spans of time.  Natural selection acts on individual organisms, which in turn can shape entire species.  Natural selection starts in a single generation, in one individual. It can take thousands or millions of years for genotype of entire species to evolve (why?).  Fossils provide solid evidence that organisms from the past are not the same as today. 14  DIVERGENT EVOLUTION  Species: Group of similar organisms that can:  Mate with each other  Produce an offspring  Offspring is able to mate  Offspring is able to reproduce  Divergent evolution: when 2 species evolve in diverse direction from common point  Natural selection results in eventual split of 1specie into 2 because they have been physically separated and exposed to diff envr, which have lead to diff adaptations & the inability to reproduce or make a fertile offspring.  Naturally, this theory led to a classification system based on morphology (physical characteristics) where organisms that were more physically alike meant were more closely related to each other 15  CONVERGENT EVOLUTION  However, morphological similarities might be explained by selective pressures of the environment. A given trait can be favorable in a given environment, which means adaptable individuals, with increased fitness, will pass on characteristics proportionately to subsequent generations as long as environmental conditions remain unchanged.  Similar phenotype can evolve independently in distantly related species because they increase fitness in a given environment.  Convergent evolution: similar traits evolve independently in species that do not share common ancestry.  In other words, individuals in a population could have a mutation that arose independently of another species and pass it on to offspring. 16  ADAPTIVE CONVERGENCE  Analogous Structures: features of different species that are similar in function, not necessarily in structure, which are not derived from a common ancestor, but in response to similar environment. 17  HOMOLOGOUS STRUCTURES  The presence of structures in organisms that share the same basic form is another type of evidence for evolution.  Homologous structures: similar physical features in organisms that share a common ancestor.  Ex: appendages of human, dog, bird and whale. 18  VESTIGIAL STRUCTURES  The presence of structures in organisms that share the same basic form is another type of evidence for evolution.  Vestigial structures: structures without functions. Appear to be residual parts from a past common ancestor.  Ex: wings on flightless birds, hind leg bones of whales or human tail bone 19  SHARED CHARACTERISTICS  Shared ancestral character: characteristic found in ancestor of group.  Shared derived character: does not include all of the ancestors in the tree.  Both terms are relative to starting point of reading relationships.  Useful to distinguish between clades in a phylogeny tree.  Organizing evolutionary relationships of all life on Earth requires use of geological time scale, along with organisms that have gone extinct. Have to distinguish between homologies and analogies, along with genetic sequence analysis.  Taxonomy is a subjective discipline: many organisms have more than 1 connection to each other, so personally have to decide order of connection.  Parsimony: assumption that events occur in the simplest way (least steps). 20  PHYLOGENY TREE  Branch point: place where an evolutionary split occurs. Represents when a single lineage evolved into a distinct new one.  Basal taxon: a lineage evolved early from root and remains unbranched.  Sister taxa: 2 lineages stemming from same branch point.  Polytomy: branch with > 2 lineages. Serve to illustrate when relationships have not been determined definitively.  Organisms in 2 taxa may have split apart at specific branch point, but neither taxa gave rise to other. 21  CLADOGRAM  Cladogram: diagram which shows the relationship between different organisms based on their similar characteristics 22  EMBRYOLOGY  Embryology: study of development of the anatomy of an organism to its adult form.  Embryology also provides evidence of relatedness between divergent groups of organisms.  Humans have tail structure during dev but it is lost by the time of birth.  Demonstrates relationship with primates outside of great apes.  Mutations in embryo can have magnified consequences in adult. 23  BIOGEOGRAPHY  Biogeography: Geographic distribution of organisms  It follows patterns best explained in conjunction with movement of tectonic plates over geological time.  Broad groups that evolved before breakup of Pangea (200 million years ago) are distributed worldwide. Groups that evolved after breakup appear unique in regions around planet.  Endemic: species found nowhere else.  Typical of islands or isolated regions preventing species migration. 24  MOLECULAR BIOLOGY EVIDENCE  Evidence of common ancestor for all life is reflected in universality of DNA as genetic material and genetic code as well as similarities in replication and expression machinery.  Relatedness of groups of organisms reflected in similarity between DNA sequences, which can be obtained from DNA Sequencing  All organisms are made up of cells & come from cells (Cell Theory)  All organism have a plasma membrane, ribosomes and cytoplasm 25  OVERVIEW  Speciation explains the diversity of organisms that inhabit Earth  All life shares genetic similarities (why?), but only certain organisms combine genetic info by sexual reproduction and produce viable offspring (species).  Microevolution: changes in allele frequencies within a population over generations  Macroevolution: leads to evolution of new species when populations diverge from common ancestor and become reproductively isolated from original population. 26  OVERVIEW 2  Allopatric speciation: geographic separation  When populations become geographically isolated, the flow of alleles is prevented.  Over time and with different selective pressures in environment, populations diverge and become genetically independent species.  Sympatric speciation: occur within a shared habitat.  Polyploidy: Serious chromosomal (extra) error during cell division to create gametes (meiosis). Wrong separation of chromosomes or chromatids.  Explains why different species can inhabit same area. More comm in plants.  In both cases, populations become reproductively isolated. 27  OVERVIEW 3  Adaptive radiation: occurs when single ancestral species give rise to many new species. Can happen when new habitats become available.  Prezygotic barriers: block reproduction prior to formation of zygote.  Ex: Different mating seasons or unique courtship behaviors  Postzygotic barriers: block reproduction after fertilization occurs.  Hybrid: an individual created from the cross of 2 different species, that is sterile (cannot procreate with either specie of parent or self to create offspring). Ex: horse + donkey = mule. 28  ABILITY TO REPRODUCE  Members of same species share both external & internal characteristics, which develop from DNA  The closer relationship 2 organisms share, the more DNA they have in common  Appearance can be misleading in suggesting an ability or inability to breed.  Hybrid: Offspring produced from an egg and sperm of 2 separate parents. Infertile: unable to successfully reproduce when reach maturity, if made from different species.  Gene pool: collection of all variations of genes in population of species.  Changes must be genetic bc only way to share and pass on traits.  Only heritable traits can evolve: changes in gametes, not somatic cells!29  SPECIATION  Presence in nature of hybrids between similar species suggest that they may have descended from single interbreeding species and speciation process not yet complete.  Speciation: formation of 2 species from 1 original species.  Allopatric speciation: “other homeland” involves geographic separation of populations from a parent species that evolves into 2 new species unable to interbreed.  Sympatric speciation: when a parent species remains in one location. 30  GENE FLOW  A geographically continuous population has gene pool that is relatively homogenous  Gene flow: movement of alleles across range of species is relatively free because individuals can move and mate with individuals in new location.  Frequency of an allele is similar across geographic distribution  When population become geographically discontinuous, free flow of alleles prevented  When separation last for long period of time, 2 populations able to evolve in different pathways  Allele frequencies gradually become different as new mutations independently arise in each population  Envr conditions: climate, resources, predators and competitors for 2 populations differ causing natural selection to favor divergent adaptations for each group. 31  GENE FLOW Gene flow: the flow of alleles in and out of population due to migration of individuals or gametes. Variable flow of individuals in and out of group changes the gene structure of the population and introduces new genetic variation to populations in different geological locations and habitats. 32  ALLOPATRIC SPECIATION  Geographic separation can occur through changes in landscape such as: new river, erosion, travel to new location without returning, floating to an island.  Dispersal: few members of a species move to new geographic area  Vicariance: natural selection arises to physically divide organisms.  The farther the distance between 2 groups that were once the same species, the more likely speciation will occur. 33  ADAPTIVE RADIATION  Adaptive radiation: many adaptations evolving from a single point of origin (founder species), causing species to radiate into several new ones.  Evolution in response to natural selection leads to different physical characteristics arising. 34  SYMPATRIC SPECIATION  A divergence taking place without the need of a physical barrier to separate individuals.  Aneuploidy: error in chromosome number (more or less)  Polyploidy: condition in which a cell or organism has extra set of chromosomes  Autopolyploidy: Incompatible with normal gametes, could self- fertilize if have means or reproduce with others of species that had same mutation.  Allopolyploid: individuals of 2 different species reproduce to form viable offspring. Happens in plants more often as animals unlikely to survive error. 35  SYMPATRIC SPECIATION  As population grows competition for food also grows.  Under pressure to find food, a group within a population has genetic flexibility to discover and feed on another resource  Omnivore vs (Herbivores or Carnivores)  Those feeding on 2nd source could remain fixed to specific location and interact mostly with those that are most similar to themselves.  Over time, genetic differences might accumulate between 2 different groups. 36  REPRODUCTIVE ISOLATION  Reproductive isolation: inability to interbreed between 2 populations.  Zygote: fertilized egg. 1st cell of development of organism that reproduces sexually.  Postzygotic barrier: occurs after zygote forms  Hybrid inviability: cannot form normally in the womb, do not survive past embryonic stages.  Hybrid sterility: Reproduction could lead to birth and growth of hybrid that is sterile and unable to produce offspring of their own. 37  PREZYGOTIC BARRIERS  Mechanism that blocks reproduction from taking place.  Includes: the prevention of fertilization.  Temporal isolation: differences in breeding schedules (season)  Habitat isolation: movement to new location no longer having overlap between 2 populations of same species. Over time, natural selection, mutation and genetic drift will result in divergence of 2 groups.  Behavioral isolation: presence or absence of specific behavior prevents reproduction from taking place.  Gametic barrier: difference in gamete cells prevent fertilization from taking place  Structural barrier: Reproductive organs are not compatible.  Structures designed to attract 1 type of pollinator can prevent access to a different one. 38  VARYING RATES OF SPECIATION  Gradual speciation model: species diverge gradually over time in small steps  Punctuated equilibrium model: new species undergoes changes quickly from parent species and remains largely unchanged for long periods of time afterward  Primary influencing factor on changes in speciation rate is environmental conditions 39  RING OF SPECIES  When new species arises, there is transition period during which closely related species continue to interact. 40  OVERVIEW Mechanisms of inheritance not understood at Darwin’s time (before Mendel) During Mendel’s time microscopes were not advanced enough to observe chromosomes. If a phenotype is favored by natural selection, allele frequencies can change, which means the population is evolving. Genetic drift: chance occurrence that some individuals have more offspring than others, which means more of their genes get passed Small populations and isolated islands are highly susceptible Allele frequencies remain stable from generation to generation if certain conditions are met: no mutations, no gene flow, random mating, no genetic drift and no selection takes place. (Real life…?) 41  OVERVIEW 2 Natural disasters can magnify genetic drift when large portion of population is killed Bottleneck effect: leads to changes in genetic structure of surviving population Founder effect: Populations might experience strong influence of genetic drift when some portion of population leaves to start new population in new location, or it gets separated by physical barrier. Both Bottleneck effect & Founder effect reduce genetic variation, which is the basis for natural selection. They also change allele frequencies. Allele frequencies can also change due to mutations and when individuals do not randomly mate, as selecting a mate based on phenotype determines genotype. These conditions can result in deviations which lead to microevolutions. 42  POPULATION GENETICS A gene may have several alleles (variants) that code for different traits associated with each character. Wild type: Most common trait of a characteristic in a population Each individual in a diploid population can only carry 2 alleles for a particular gene Allele frequency: proportion of a specific allele within a population relative to all others present in that population. Evolution: a change in the frequency of an allele in a population. Allele frequency can change depending on environmental factors (How?) Natural selection can alter a population’s genetic makeup (How?) Gene pool: sum of all the alleles in a population. 43  GENETIC VARIANCE Natural selection + evolutionary forces can only act on (genetic) heritable traits Beneficial traits or behaviors are selected for, deleterious alleles are selected against. Acquired traits are not heritable. Changes accrued through lifetime called (?) D Heritability: fraction (why?) of phenotype variation that can be attributed to genetic differences/variance among individuals in a population. The greater variety of a population, the more susceptible it is to evolutionary forces that act on heritable variation. Genetic variance: diversity of alleles and genotypes within a population. 44  INBREEDING Inbreeding: mating of closely related individuals, which can have undesirable effects of bring together deleterious recessive mutations that can cause abnormalities and susceptibility to diseases. Parents with 1 defective copy of a gene (C?) When 2 defective copies of a gene are passed down to the offspring and it results in their death (LR?) Inbreeding depression: carriers interbreeding increase likelihood of producing diseased offspring. In healthy population, chance that 2 carriers will mate is low, natural selection will not be able to swiftly get rid of allele, it can be maintained at low levels in gene pool. 45  GENETIC DRIFT Evolutionary sources: natural selection, genetic drift, gene flow, mutation, nonrandom mating and environmental variances. With natural selection, individuals more likely to survive and have more offspring, passing on more of their genes to the next generation. Selection pressure: driving selective force. Genetic drift: the effect of chance. Some individuals will have more offspring than others, not due to advantage by genetics, but random occurrence: right place, right time or wrong place, wrong time. Over time, it can completely eliminate an allele from population or give it a boost in frequency %. Small populations are more susceptible. Large populations buffer chance (Why?) 46  BOTTLENECK EFFECT Bottleneck effect: a chance event or catastrophe that can reduce the genetic variability within a population. A natural disaster that kills, at random, a large portion of the population (and genome!) can magnify genetic drift. In one instant, genetic structure of survivors becomes genetic structure of entire population, which might be very different from pre-disaster. 47  FOUNDER EFFECT If a portion of population leaves to start new population in new location or if population gets divided by physical barrier it may experience genetic drift. Individuals moving unlikely to represent frequency of alleles of overall population. Founder effect: occurs when genetic structure changes to match founding individuals. Sounds like Founder… S? 48  NONRANDOM MATING Non-random mating can result in a genetic structure change in population Traits that lead to more mating for an individual are under the influence of natural selection. Assortative mating: individual’s preference to mate with partners who are phenotypically similar to themselves. If the population is spread out over large geographic distances, individuals do not have equal access to one another. 49  ENVIRONMENTAL VARIANCE Cline: type of geographic variation where populations of a given species vary gradually across an ecological gradient. Latitudinal cline: Organisms living closer to poles have different adaptations. Example: conserve heat better. Altitudinal cline: Organisms living at different heights with respect to sea levels. It is due to gene flow taking place between populations. Could lead to ring of species. Restricted gene flow could lead to abrupt differences, even speciation. 50  OVERVIEW  Natural selection acts on level of individual, selecting those with higher fitness (reproductive success) compared to rest of population.  Natural selection favors most adaptive variation for a specific environment. Stabilizing selection: if environment is stable, there will be an overall decrease in variation of population. Directional selection: shift population’s variance toward new, more favorable phenotype. Diversifying selection: increase variance by selecting for 2 or more distinct phenotypes.  Sexual selection: when one sex has more reproductive success than the other, leading to phenotypic differences known as sexual dimorphisms due to different selective pressures.  Evolution has no purpose, it is sum of various forces that influence genetic and phenotypic variation of a population.  Why is there no “perfect” organism? 51  STABILIZING SELECTION When natural selection favors an average phenotype. It selects against extreme variation. Example: organisms that blend in with surroundings are less likely to be spotted by predators. Results in population’s genetic variance decreasing. 52  DIRECTIONAL SELECTION Happens when the environment changes Phenotypes at one end of the spectrum are selected Flowers grow taller so rabbits cannot get to them near floor 5  DIVERSIFYING SELECTIONS 2 or more distinct phenotypes can each have their advantage and be selected by natural selection, while intermediate phenotypes are less fit. Large, alpha males claim territory & Small males can sneak in alpha territory Medium-sized males are at disadvantage because cannot due either Can also occur when environmental changes favor individuals at either end Example: for individuals that live in environment with 2 different colors, is better to have 1 color or another. Blend of colors results in not beneficial in either place. Results in increased genetic variance as population becomes more diverse. 54  FREQUENCY-DEPENDENT SELECTION  Favor phenotypes that are common (positive) or rare (negative)  Orange male lizards are strongest and can fight blue (medium)  Yellow are smallest and pass of as females, can sneak past orange, but not blue  Results in populations cycling through phenotype distribution  Negative serves to increase population’s genetic variance by selecting for rare phenotypes and positive does the opposite. 5  SEXUAL DIMORPHISMS Aside from reproductive organ differences, males are often larger and display more elaborate colors. These differences known as sexual dimorphisms. There is more variance in reproductive success of males than there is female. It generates a strong selection pressure among males to get mating, resulting in evolution of bigger body size and elaborate patterns. Females get handful of mates, able to select more desirable males/traits Rarely, roles could be reversed, and females are the ones with more variance 5  SEXUAL SELECTION Sexual selection: the selection pressures on males & females to obtain mating It can lead in development of secondary sexual characteristics that does not benefit individual’s likelihood of survival, but increases reproductive success. Handicap Principle: theory of sexual selection that argues only fittest individuals can afford costly traits. Example: large colorful feathers help reproduction, but decrease survival bc easier to be spotted by predators. Females like it bc mean was able to escape. Good gene hypothesis: males develop impressive ornaments to show efficient metabolism or ability to fight disease. Females choose most impressive traits as it signals genetic superiority they can pass down to offspring. 57  NO PERFECT ORGANISM Fewer, but healthier offspring may incr chances of survival vs many weak offspring. Honest signal: trait that gives truthful impression of individual’s fitness Natural selection can only select on existing variation in a population, new alleles from mutation and gene flow. Natural selection acts at the individual level, taking under consideration beneficial and unfavorable alleles as a net effect for fitness determination. Linkage disequilibrium: some alleles are linked due to physical proximity in genome making it more likely they will be passed on together. Natural selection constrained by relationship between polymorphs. Medium beneficial does not want to go through most disadvantage stage to eventually have offspring that are most advantageous. Not all evolution is adaptive bc genetic drift & gene flow often counteract natural selection. Evolution has no goal. Not moving towards ideal organism. Sum of all forces. 58