Chapters 2-8 Power Points PDF

Chapter 2: Descent with modification Microevolution- a genetic change in a population of organisms either due to natural selection, or genetic drift. Macroevolution- where a new species is formed (may take thousands of years). Evidence of change, example: Soapberry bugs (native to...

Chapter 2: Descent with modification Microevolution- a genetic change in a population of organisms either due to natural selection, or genetic drift. Macroevolution- where a new species is formed (may take thousands of years). Evidence of change, example: Soapberry bugs (native to Florida & Caribbean) ○ Long mouth parts to eat large fruit seeds ○ ○ ○ Overall beak length of this population of birds has decreased over time following the introduction of FPGRT. Indicates that birds with shorter beak length had the advantageous trait due to food sources available. The population evolved to have shorter beak length Vestigial Structures – functionless or rudimentary version of a body part that has an important function in other closely allied species. ○ Example: Whale pelvis and Arrector pilli muscle (on hair follicle) Extinction: Natural process of evolution ○ Fossils and fossil records provide evidence showing traces of organisms that lived in the past Law of succession: animals that currently inhabit an area will show a resemblance to the fossils in the same area ○ Shared characteristics and distributions of species follow the movement of continents  Transitional forms “missing link”: Morphological characters of two major groups found in the same organism. ○ Usually missing from the fossil record ○ Example: reptile and birds Homology: The same organ in different animals under every variety of form and function ○ Example: Metacarpals in humans, bats, whales, and horses. All have but used for different function Analogy: These organisms have similar structures, which have similar functions, but they were not inherited from a common ancestor. ○ Example: Shark and Whale Reverse transcription: RNA that is transcribed into DNA and sometimes inserted back into the nuclear genome. ○ Central dogma DNA → RNA: transcription RNA → protein translation Retrotransposons: retrovirus like DNA that reverse transcribes itself into the genome many times. Considered to be “garbage” DNA. Intron: non-coding sections Exons: coding sections that must be removed before translation Pseudo genes: nonfunctional copies of normal genes that originate when mRNA is accidentally reverse transcribed back into the genome. Radiometric dating: analyzes the decay of radioactive isotopes within rocks and fossils, which occurs at a predictable rate, allowing scientists to calculate the age of the material. Chapter 3: Darwins postulates: ○ Variation: Individuals within a population are variable ○ Inheretance: Some of that variation is passed from parents to offspring (heritable) ○ Over production: In every generation, some individuals are more successful at surviving and reproducing ○ Non-random survival and reproduction: Survival and reproduction of individuals are not random but tied to variation in individuals. Those better at surviving are naturally selected. Testing postulates: Snapdragon ○ Was the trait variable? Yes, started with 75% white and 25% yellow ○ Was some of the variation heritable? Yes, next generation showed 77% white and 23% yellow ○ Did individuals in the population vary in their reproductive success? ○ Was reproduction non-random?  ○ Did the population evolve? Testing postulates: Finches ○ Beak sizes show heritability and adaptation. ○ ○ Is this trait heritable? Yes, increased beak size over time ○ Do you see a strong correlation between parent beak size and offspring beak size? Yes ○ What has happened here? La nina effect: Gets cold and dry, birds stock up on seeds Darwinian fitness: individuals ability to survive and reproduce ○ Measured by: number of successful offspring, number of offspring, and number of gametes produced ○ Surrogates (replacements) for fitness: physical size, energy reserves (fat or glycogen), number of flowers per plant, etc Adaptation: trait increasing fitness relative to other organisms ○ Example: Panda thumb: anatomy changed overtime: Seasmoid bone allows them to hold and shred bamboo Chapter 4: Homoplasy: A shared characteristic that is not due to a common ancestor, but rather evolved independently in each species. Homoplasy often results from convergent evolution. For example, the wings of insects, birds, and bats are all used for flying, but they are structurally different.  Convergent evolution: two traits resemble each other but do not share a common ancestor Reversal: derived trait due to mutation, returns to ancestral form *Phylogeny worksheet from class* Monophyletic: Ancestor and ALL descendants Paraphyletic: Ancestor and SOME descendants Polyphyletic: NO ancestor and some descendants Polytomy: 3+ on a node Parsimony: Simplest explanation/ least number of changes Bootstrapping can evaluate the consistency of branches among trees; sampling with replacement Phenetic approach (classic): groups classified by kingdom, class Cladistic approach (new): Only monophyletic branches get names. Paraphyletic branches do not get named. Biogeography: Tracking organisms by their geographic location ○ Follows the idea of succession = individuals from an area should be more closely related to each other than to other continents. Molecular clock: a method used to estimate the time since two species diverged from a common ancestor by comparing the differences in their DNA or protein sequences Coevolution: occurs when species evolve together. Coevolution happens in species that have symbiotic (long-term interactions between two different species) relationships. ○ Examples: flowering plants and their pollinators. Which one can be acted on by natural selection? ○ Phenotype What other aspect of genetics could interfere with selection? ○ For selection to work, phenotype has to be controlled by genes; it has to evolve with genetic variation, NOT environmental Genetic diversity: total number of mutations that exist in a locus Why is genetic variation important? ○ Conservation biologists consider genetic variation a level of diversity, similar to species diversity, or ecosystem diversity. Explain why this is important? ○ Genetic drift: random change in allele frequencies in a population over time (evolution by random change) Lizards: ○ Environment affects if male or female (lizards have genotypes for both) ○ NS only acts on males ○ Genotype not expressed until reaches certain temperature ○ ^Phenotypic plasticity: genotypes change in response to environment Chapter 5: DNA mutations ○ Synonymous/silent: Changes coding sequence, NOT amino acid sequence ○ Non-synonymous: Changes amino acid sequence ○ Point: single nucleotide base is changed can result in Substitution: swapped for another Insertion: add new nucleotide Deletion: nucleotide removed ○ Nonsense: Causes STOP codon Induced response: changes in an organism that occur in response to a threat, such as an attack Unequal crossing over: Happens during meiosis from natural selection Chapter 6: HW equilibrium Assumptions of H-W: ○ No Natural Selection ○ No Mutation ○ No Migration ○ No chance events (genetic drift) ○ Mating is random (gene pool model of mating) Chapter 7: Greater prairie chicken example lekking species – species where males gather in a communal area to perform courtship displays to attract mates, while females choose their mates blue = preferable habitat (long grass prairie) ○ territory was removed, so population was decreasing ○ number of males was decreasing, thus they could not mate – now they are monitored cousins and siblings were breeding with each other because there was no other option wisconsin bird were transported to illinois – human mediated migration ○ alleles were brought with them – new alleles were brought into the population and rescued the population from inbreeding the greater prairie chicken population was evolving, not due to natural selection habitat was increasing, population size was decreasing What is happening? inbreeding occurred, but it was rescued by the migration and the addition of new alleles island continent example — migration can change allele frequencies and violate HW equilibrium – it is possible! migration – the movement of alleles between populations ○ migration = gene flow ○ can be caused by anything that moves alleles far enough to go from one population to another Adding migration to H-W analysis - gene flow as a mechanism of evolution ○ figure 7.1 – alleles arriving on the island from the continent represent a relatively large fraction of the island gene pool, whereas alleles arriving on the continent from the island represent a small fraction of the continental gene pool ○ figure 7.2 – migration, in the form of individuals arriving from a continental population fixed for allele A2, increases the frequency of allele A2 in the island population this diagram follows an imaginary island population of mice from one generation’s gene pool (initial allele frequencies) to the next generation’s gene pool (final allele frequencies) the bar graphs show the number of individuals of each genotype in the population at any given time ○ A single bout of random mating will put the population back into Hardy-Weinberg equilibrium for genotype frequencies **migration is a potent mechanism of evolution. in practice; migration is most important in preventing populations from diverging the northern water snake example — mean snakes – empirical research on migration versus selection migration will homogenize allele frequencies across populations unless it is balanced by another mechanism of evolution hunt in water, so they get cold easily subspecies (ESU’s - evolutionary significant units) – individuals vary in appearance, color pattern is determined by a single locus with 2 alleles, and the banded allele is dominant over the unbanded allele ○ main land variety – camo, blotchy patches of brown on dark green - helps hide them when they are in leaf litter – banded ○ island variety – almost black, melanin type - adaptation to get warmer faster – unbanded no natural selection pressure on the camouflage local natural selection for the alleles that promote the melanin phenotype out on the islands, has higher fitness on the island  ○ among very young snakes, unbanded individuals are more cryptic on island rocks than are banded individuals ○ the youngest and smallest snakes are presumably most vulnerable to predators ○ on the island, unbanded snakes indeed survive at higher rates than banded snakes on the mainland, the phenotype that has a higher fitness is the camouflage – if selection favors unbanded (island) snakes on the islands, then we would expect that the island population would consist entirely of unbanded snakes… why is this not the case? ○ in every generation several banded (mainland) snakes move from the mainland to the islands – migration of individuals from the mainland to islands appears to be preventing the divergence (due to selection) of island versus mainland populations the migrants bring with them copies of the allele for banded coloration ○ *when the migrant snakes interbreed with the island snakes, natural selection is acting as an evolutionary mechanism in opposition to migration, preventing the island population from being driven to the same allele frequency seen in the mainland population figure 7.6 – these histograms show frequency of different color patterns in various populations. ○ category A snakes are unbanded (island population); categories B and C are intermediate; category D snakes are strongly banded (mainland population) what does that mean? Perforated barrier to natural selection ○ have unfit alleles that migrate/are brought into a local population – outbreeding (mating among unrelated individuals) unfit alleles that are causing a decrease in fitness – outbreeding depression ○ outbreeding vs. migration – if alleles frequencies are already the same, that is migration - random differences in allele frequencies, that is outbreeding difference in local selection within the island mainland favors D form island favors A form migration – outbreeding is occurring - selection has to be VERY strong when its both local selection and migration (continues to bring in unfit alleles) Selection and migration – figure 7.7 - the combined effects of selection and migration on allele frequencies in island water snakes strong selection, little migration = as q is becoming more common, the allele is changing in the population rapidly moderate selection, moderate migration = the change happens more slowly  ○ curve (b) shows that if q is greater than 0.05 and less than 0.93 in this generation, then q will be larger in the next generation weak selection, lots of migration = the change happens VERY slow, but the alleles can go back and forth (there can be no change over time) - there are points of equilibrium migration can work against selection - can have outbreeding and outbreeding depression example - outbreeding salmon to ALMOST death – each breeding site is under local selection for certain alleles. But when sampling adults, salmon live in a big population together but aren’t mating (anadromes – live their adult cycle in large body of water, but bred at local sites) so when they were put in smaller stream, they all died because there was local selection Gene flow and selection – Remember populations are the units where natural selection causes evolution Individual populations of the same species can be selected for different traits, this is sometimes called local natural selection gene flow (migration) will have a tendency to homogenize traits if there is different local selection for some populations gene flow among populations will work against selection ○ **local selection must be very strong to overcome gene flow gene flow/migration can bring in unfair alleles, fir alleles, ot neutral alleles depending on local natural selection outbreeding – alleles come into a population via migration outbreeding depression – if these alleles cause a drop in fitness genetic drift, and migration another way that populations can evolve is by genetic drift – the change in allele frequencies in a population by chance events ○ happens during mating, only a portion of the gene pool actually involved in reproduction ○ probability estimates that the chances of the same proportion of alleles being passed on are small ○ figure 7.8 – chance events can alter allele and genotype frequencies - genetic drift, in the form of sampling error in drawing gametes form the initial gene pool small populations are more prone to rapid change due to genetic drift ○ small populations are common during colonization ○ in a small population, chance events produce outcomes that differ from theoretical expectations sampling error = this kind of random discrepancy between theoretical expectations and actual results  sampling error in the production of zygotes from a gene pool = random genetic drift OR genetic drift genetic drift cannot produce adaptation because it is nothing more than a cumulative effect of random events ○ **in populations of finite size, chance events – in the form of sampling error in drawing gametes from the gene pool – can cause evolution genetic variation within populations Variation within populations is measured using the either allelic diversity (A), percent polymorphism (P) or average Heterozygosity (observed) or H some markers cannot be used to calculate this so you will also use molecular diversity (pi symbol) or the mean of the number of haplotypes Bottleneck = a situation where a population drastically decreases in size due to a sudden event like a natural disaster, overhunting, or habitat destruction, leading to a significant loss of genetic diversity within that population as only a small, random sample of individuals survive to reproduce, making the new population genetically less diverse than the original one Variation among populations – when allele frequencies vary among populations population genetic structure is simply the proportion of alleles or genotypes that are shared among sampled groups ○ measures how alleles differ across populations the less sharing there is, the more structure you have FST – structure in population genetics is measured using this proportion ○ Is a measure of how different each population is genetically from another (at maximum migration among populations FST will approach 0.00) ○ compare allele frequencies in sub species to the total population ○ when FST = 0, (Panmixia – when everyone is mating with everyone else, mass amount of migration) all allele frequencies are the same ○ as allele frequency differs, FST goes up – will go to 1 fewer alleles or genotypes will be shared when populations don’t share migration patterns of genetic variation populations that are furthest apart share least number of alleles populations that are closest share a high number of alleles isolation by distance 1. figure 9.32 - southern vs northern populations of the same species more difference among the southern populations over a shorter distance – slope is increasing rapidly – more and more genetic distance  ○ the slopes reveal that southern populations are genetically more different than northern populations northern populations have a smaller slope – less genetic difference what does this mean? local selection, the north had recolonization after the ice age (after glacier receded) (difference in age of northern and southern populations) 2. figure 9.33 - geographic variation in mtDNA in warbler yellow circle - colonization – founders effect in genetics (how it looks) – everyone's the same blue circle – lots of genetic variation but not common within populations ○ could be from yellow population that was pushed south and recolonized north after the glacier receded blue circle/southern population was environmentally stable VNTRs or Microsatellites VNTRs are non-coding DNA that has no purpose – change the length of DNA chain and makes new alleles ○ DNA is measured through SIZE – small moves through fast, large fragments move slowly measures like genotypes from genetics… 2 small/half peaks = heterozygous, 1 large peak = homozygous can look at the presence or absence of alleles within populations – can see shared alleles if there is migration, should have the same VNTRs in a population if they are mating with each other ○ If they are in isolation, they will have unique VNTRs to that population Microsatellites = regions of noncoding DNA with many easily identifiable alleles ○ The alleles are distinguished by the number of times a short sequence of nucleotides is repeated patterns of genetic variation assignment test of alleles in a population – looks for structure in highly variable loci (do i see alleles that are unique to certain populations?) bars with half and half – was not successful at determining a specific allele ○ colors determine uniqueness the more the colors are falling out by region, we can see the barriers to migration collard lizards – endangered species in Missouri (bad habitat – they need hot, sunny habitats) sampled at 3 loci  ○ MDH (2 alleles, Slow & Fast), MtDNA (A—D, 4 nucleotide differences), rDNA (I—III, highly conserved gene that had 3 single base differences) fixed for fast – multi locus haplotypes show that almost all were fast what is the genetic diversity within each population? they are FIXED at a multi locus haplotype in each population ○ why? habitat preferences – lizards like rocky remnant outcrops BUT Missouri changed as population changed (more forests) ○ solution was to cut corredors and the lizards started to move to the rocky outcrops and outbred Figure 7.19 – genetic variation of Ozark glade populations of collared lizards ○ Confirmed that most loci were fixed for a single allele and that genetic variation should be very low Chapter 8: Ne is called the effective population size and is the actual number of reproductive adults Ne is always less than N (population size) because not individuals are capable of reproducing Number of years to reproductive age ○ The higher the years, lower the Ne Average age in the population (demographics) Non-random mating or sexual selection (deer, birds are good examples) Ne (MTDNA) ¼ Ne (genomic DNA) ○ Y chromosome is evolving faster because its drifting because Ne is smaller ○ Effective population size is important to know population size  ^Inbreeding (low genetic diversity) is the worst for populations Outbreeding: Migration Outbreeding depression: Unfit alleles are brought to population If they act independent from each other—linkage equilibrium If not independent - linkage disequilibrium Why is linkage important? Knowing the relationship among loci on a chromosome can be a hint into the history of that gene ○ New mutations will be in linkage disequilibrium, associated with loci What are the costs of sex(ual reproduction)? Think pair share: Take five minutes and estimate why there is/are cost(s) to sexual reproduction? ○ It takes time - Have to find someone to reproduce with ○ Takes energy - ○ Have to depend of someone else to pass down ○ Predation ○ 50% dont produce offspring ○ Only pass on 50% of fit alleles ○ Only 50% of population reproducing Offspring allele combinations may be unfit ○ Genetic combinations ○ Genetic variation What are the costs of non-sexual reproduction? ○ Less genetic diversity - 100% of the alleles (clone; theyre the same) ○ Will pass down unfit alleles (unfit mutations are passed on) ○ Finding a mate ○ What are the benefits of both? ○ Can produce a lot of offspring “red queen hypothesis”: have to evolve as fast as others or you will fall behind