Biology 1001A Outcomes

Lectures 13-24
Study Notes for the Final on December 13th 2011

Lecture 13
Genetic variation: variation in alleles of genes occurs both in and among populations. Provides raw material for natural selection Brought about by mutations high genetic variation o high fitness o high evolutionary potential Constrains on Selection: Trade Offs: exchange for one thing in return for another (peacocks tail, good for the ladies but takes a lot of energy and more vulnerable to predators) Time: adapt to the past not the current ( the bird who migrates when the insect population is high but because of higher temperatures the insects population is highest at a different time so when they migrate they have no food) No Variance: selection requires variation, low long term evolutionary potential therefore they cannot evolve with the changing environment low natural selection (cheetahs bottleneck) Genetic Correlation: Genetic correlation is the amount of difference that two traits share due to genetic causes. Outside the theoretical boundary case of traits with zero heritability, the genetic correlation of traits is independent of their heritability Polymorphic locus: a location on a gene that had a large number of different sequences (many possibilities for s genotype) Fixation of Alleles: an allele becomes fixed in a population when its frequency reaches 100% (every individual in the population has that allele) Direction Selection: a mode of natural selection in which a single phenotype is favored, causing the allele frequency to continuously shift in one direction Stabilizing Selection: genetic diversity as the population stabilizes on a particular trait value Favors intermediate variants Reduces phenotypic variation Disruptive Selection: describes changes in population genetics in which extreme values for a trait are favored over intermediate values. In this case, the variance of the trait increases and the population is divided into two distinct groups. This evolutionary process is believed to be the driving force behind sympatric speciation Positive vs. Negative frequency-dependent selection: Negative frequency-dependent selection o Favors rare forms o Increase genetic variance o Rare becomes old over time and the old common becomes rare o Selective advantage of being rare (odd)

Positive frequency-dependent selection o Common forms are favored o Virtue lies in having the more common phenotype o Gets rid of genetic variation Low fitness Rare eventually disappear

Why are most genetic disorders associated with the recessive allele? Recessive are not expressed as often o selection cannot remove all copies if recessive alleles recessive alleles become hidden and carried in heterozygous genotypes

Lecture 14 and 15
Mutation: random spontaneous mistake in DNA synthesis can be harmful (HIV) or neutral (no effect) source of genetic variation converts all alleles into another o creates a new one o change alleles frequency Migration (Gene Flow): the movement of alleles between populations keeps introducing new alleles equalizes frequencies when there is a lot of migration because it alleles become more similar in other groups More genetic variation Genetic Drift: random sampling error (random deviations from expected results) one allele becomes fixed while others are lost reduced amounts of genetic variation the larger the population the smaller the genetic drift Bottle Neck: population size decrease because of a lost allele and the ability to evolved/adapt (cheetahs) Founder Events: small number of individuals finding a new population o less genetic diversity in founding individuals Non-random Mating: assortative (individuals mate with others who look like them)/disassortative (opposites attract) mating versus inbreeding/outbreeding genotype no predictable out of Hardy-Weinberg Equilibrium Effects of nonrandom matting

Selection, mutation, migration, drift, nonrandom matting all take

populations out of HWBE Some generate heterozygote deficit, others generate heterozygote excess Inbreeding: breeding of related individuals within an isolated or a closed group of organisms or people. Asexual vs. Sexual reproduction: Finding mates is a lot of work Sexually transmitted diseases Costly meiosis only half genome (alleles) Cost of males (two fold cost of sex) Asexual (cloned) females should quickly win over sexual females unless sex improves the quality of younge. Parthenogenesis: reproduction in which an unfertilized egg develops into a new individual, occurring commonly among insects and certain other arthropods Vegetative Propagation: production of a new plant from a portion of another Fission: An asexual reproductive process in which a unicellular organism divides into two or more independently maturing daughter cells Dioecious: having male and female organs show up on two different individuals of the same species (humans) Monoecious: hermaphrodite Sequential: starts out one sex and then becomes another o Potandry: That condition in which an animal is first a male and then becomes a female. o Protogyny: producing female gametes before male ones Simultaneously: both sexes at the same time Size-advantage Model of Sex change: states that reproductive functions are carried out better if the individual is a certain size/age. Assuming that the reproductive functions of one sex are better performed at a certain size, then an organism would assume the sex that its size allows to perform the best. This would increase its reproductive potential and fitness Ruby in the Rubbish Hypothesis: over time the average number of mutations in an asexual lineage will increase, sex can be beneficial because sex can continually recreate the fitter genotype Lottery Principle: any female in a constant environment will be confident that they are well adapted and know that it would be better to just clone themselves, if the environment is changing then the female would do better to produce younge that are genetically diverse and make it more likely that at least some of her younge would be well adapted to the environment Red Queen Hypothesis (Alice in Wonderland): host organism co-evolving with their natural enemy you have to continually evolve to stay in your natural place via your enemy.

Sexual Selection: selection driven by competition for mates, adjacent to natural selection Sexual Dimorphism: diagnostic morphological differences between the sexes

The sex which invests the most in producing offspring becomes a limiting resource over which the other sex will compete.

Intrasexual Selection: involves characteristics which affect the outcome of competition among members of one sex for access to members of the other sex. Intersexual: influence the evolution of secondary sexual characteristics which determine the relative "attractiveness" of members of one sex to the other sex Sex-role reversal: males give the most parental care Anisogamy: Relating to a type of sexual reproduction in which the reproduction cells are dissimilar in some respect (as size or shape). Potential vs. Average fitness: The concept of fitness is central to natural selection. In broad terms, individuals that are more "fit" have better potential for survival, as in the well-known phrase "survival of the fittest". Though natural selection acts on individuals, the effects of chance mean that fitness can only really be defined "on average" for the individuals within a population. The fitness of a particular genotype corresponds to the average effect on all individuals with that genotype. Very low-fitness genotypes cause their bearers to have few or no offspring on average

Lecture 16
Morphological Species Concept: a species defined on how the animals look Problems: qualitative variation, different looks between male and female Biological Species Concept: interbreeding capabilities Prezygotic: prevents copulation o Temporal: not sexy at the same time o Ecological: different habitat o Behavioural: not attracted to each others behavior (bird dance, or colours dont appeal) o Mechanical: doesnt fit and prevents the transfer of sperm Postzygotic: after copulation o Hybrid inviability: hybrid is born dead or never reaches maturity o Hybrid sterility: hybrid cannot produce young o Hybrid breakdown: first generation (F1) hybrids are viable and fertile but further hybrid generations (F2) are sterile Problems: extinct species, ring species, allopatric, asexual organisms Phylogenetic Species Concepts: evolutionary history Allopatric: animals live/occur in different places (not together)

Ring species: neighboring species can easily interbreed but the end species are to distantly related to interbreed Speciation that occurs parapatric: overlapping geographical zones of genetic contact Speciation that occurs sympatric: geographic isolation of a population

Speciation: forming of species Achieving reproductive isolation Allopatry o Isolation: physical barrier like the building of a new road or a glacier to prevent gene flow o Divergence: two populations become genetically different o Secondary contact: species comes into contact after being separated o Reinforcement: direct selection favouring Prezygotic isolating mechanism o Hybrid swarms: population that havent diverged much resume interbreeding o Reverse speciation: where speciation reverses (the fish interbreeding in the murky water) Island Speciation Isolation, small population, different isolation pressures, allopatric speciation, hot beds

Lecture 17
Phylogeny: an attempt to reconstruct the pattern of ancestor regulation of life on earth Node (branching point): change (new trait) Homologus traits: true phologeny similarity do to a common ancestor (ansestorial traits) Homoplasy: misleading traits Convergence: misleading simularity simular but no recent common ancestor Divergence: misleading dissimilarity look different but common ancestor Synapomorphy: traits shared by two or more groups both inheritted by a common ancestor Derived Traits: recents evolutionary origin (not present in the out group) Ancestorial Traits: present in the out group or common ancestor Outgroup: oldest ancestor (usually most different)

Parsimony: phylogeny requiring fewest evolutionary steps assumes similarity due to convergence (many steps) is rarer than similarity due to a common ancestor (fewer steps) Monophyletic: includes all descendants of most common ancestor Non-Monophyletic Group: doesnt include all descendants Cladistics: a system of classification based on phylogenetic relationships and eolutionary history of groups or organisms. Automorphies: derived trait unique to a terminal group Most Parsimonious: fewest number of evolutionary steps Every time a new trait is introduced represents a evolutionary step Principles of Phylogenetics: evolutionary relationships reflect how recently groups shared a common ancestor Reconstruct phylogenies using similarity Similarity usually reflects recent shared ancestry (homology)

Lecture 18
Superposition: top rock layer is new than the layers underneath it Relative Order: fossils found on the bottom layers on rock are older than the fossils found on the top. (not absolute dates) Radioactive Dating: parent decays to daughter isotope at a predictable rate (counts the half-lives to estimate absolute age) Number of half-lives x Length of half-life = absolute age Anagenesis: change without speciation (distinct branching events) Cladogenesis: associated with branching events, one species to a recognizable two species in fossil records. (with branching events) Gradualism: lineages are always changing The gaps in the fossil record are because the fossils werent preserved Punctuated equilibrium: periods of rapid change and long periods on stasis (no evolutionary change) The gaps in the fossil record are there simply because there was no change.
The fossil record isnt perfect because of huge gaps within it. These gaps are said to be due because some animals preserve better than other. The fossil record is also said to be bias because some environments are better at preserving fossils than others therefore there is more of those animal than any other (marine animals)

Living Fossils: animals who havent evolved and are almost identical to their ancient ancestors fossils Copes Rule: over evolution species increase body size Individual-Level selection: evolution increases body size to benefit the individual (more available food, safer from predators) Species-Level selection: evolution increases body size to benefit the entire species (a species may be less likely to go extinct) Passive floor effect: nowhere to go but up Exceptions Insects or anything with an exoskeleton Upper limit (cannot physically get any bigger) Extinct lineages didnt follow copes rule in terms of the horse who was said to be a good example

Lecture 19
Ecology: interactions between organisms (abiotic is non-living and biotic is living) Biodiversity: is how many different species are present in a given area Speciation increases the number Extinction decreases the number Adaptive radiation: extreme speciation over a short period of time Evolutionary innovation: new adaptions arise making a species stronger allowing them to go to another environment or become more efficient (promotes adaptive radiation) Background extinction rate: standard rate of extinction Mostly low, but never zero Extinction risk independent of how old a given species is Some groups are more extinction prone than others Human impacts are creating the 6th mass extinction to occur on planet earth o Hunting, new species introductions, habitat, climate change Mass extinction: a large number of species go extinct over a small period geological time, usually created by a catastrophe like a meteor hitting the earth or weather changes and animals cannot adapt quickly enough Evolutionary arms race: the levels of defense and counter defense will continue to escalade, animals adapt to beat a predator and the predator counter adapts Evolutionary advantages Life-Dinner Principle prey run for their lives while the predator runs just for food therefore the prey have a higher fitness Population the higher the population the more chance it has for a mutation Generation time the shorter the generation time the quicker the species can evolve

Red Queen Equilibrium (red queen from Alice and wonderland, no matter how fast Alice ran she went nowhere): organisms must adapt to stay in the same strategic position relative to their enemies who will change relative to their prey Prudent Parasite Hypothesis: virulence (extreme harmfulness) is harmful to the parasite therefore the parasite should only be harmful if they recently colonized a new host Trade-off hypothesis: virulence had costs and benefits o Optimal virulence depends on ecology of host and parasite Transmission mode hypothesis: optimal virulence depends on how the parasite moves between hosts o Direct contact: not as good as indirect (vectorborne) Insect vectors are indirectly spread (Low population = low variance)

Lecture 20
Population: group of individuals of the same species living in a defined geographical area (boundaries in which a population is given) Allele frequencies, genotype frequencies (genetic diversity) Population size (N) Sex ratio male vs. female Age structure (pre reproductive vs. reproductive vs. post reproductive) Rate of growth factors How to Find a Population Size Humans can simply sign a form (count) Things that dont move can be counted Sample Size multiplied by Area Mark Recapture o Capture and mark initial (M) MC o Capture second sample (C) see how many are marked (R) R o Use to estimate population size (N) o Assumptions: only works if Marked and unmarked are equally likely to get caught Marks dont wear off or affect animals survival Time between initial capture and re capture needs to be perfect Long enough to mix freely with unmarked animals but not so long that the population size changes

N=

Density = population size (N)/area or N/Volume Influences access to resources o Too high of a density and populations man decrease o Too loo of a density and population size may decrease as well

Dispersion

Group living: Pros more mates, more protected Cons Low resources, more noticeable to predators Generation Time: low = high population high = low population Sex Ratio: the sex who gives the younge the most parental care is less than the sex that gives the least amount of parental care to the younge

Lecture 21
Age Structure: Prereproductive vs. Reproductive vs. Postreproductive Life Table: a table of summarized survival and reproduction for a cohort (a large number of individuals treated as a distinct group) of individuals. Age Specific Mortality Rate: what proportion of the individual is alive at the beginning of that time interval to the proportion that is still alive at the end Age Specific Survivorship Rate: opposite of the mortality rate Survivorship Curves Type 1: typically larger animals, invest a lot in parental care Type 2: typically smaller animals, most dont die from old age death is not relative to age Type 3: produces the most young although most of the initial population doesnt live long but when it reaches a threshold they continue to live

Life History: balancing energy or resources given competing demands Growth Reproduction (trades offs many young or few young with a lot of parental investment) without reproduction there is no fitness, but is energetically costly Self-maintenance (repair) healing wounds Everything devotes its energy or/and resources to some combination of these three things The way that they balance these demands is called their life history strategy varies with species varies within a species due to ecological conditions o environments have different needs and species in that environment will channel their energy and resources to what is needed (r)-Selected Species: e.g. mouse QUANTITY invests high in reproduction reproduces at an early age short life span high levels of mortality many younge dont make maturity invest little per younge B = number of births b = per capita birth rate D = number of deaths d = per capita death rate E = emigration I = immigration r = intrinsic growth rate N = population t = time K = carrying capacity (K)-Selected Species: e.g. humans QUALITY Devote more energy to growth and repair Longer generation time Takes longer to mature Produces small amount of younge High parental investment

Modeling Population Growth N = # of births (and immigrations) - # of deaths (and emigrations) N/t = (B+I) (D+E), per unit time Per capita death rate d = D/N Per capita birth rate b = D/N

Intrinsic growth Rate r = (births/N) (deaths/N) example a small town in Kenya starting with a population of N = 100 60 babies born each year (b= 60/1000= 0.06) 30 deaths each year (d= 30/1000 = 0.03) r = (0.06-0.03) = 0.030 or 3% Net change of 30 people / year In the exponential model of growth, r is independent of population size Exponential Growth Rate dN/dt = rN o grows is r is greater than zero o shrinks if r is smaller than zero For any given population, in any given environment, there may be a maximum number of individuals the environment can sustain which is known as the carrying capacity.

Logistic model: as N increase, dN/dt decrease o (K-N)/K = growing room As N K, (K-N/ K) 0 dN/dt = rN (K-N)/K

Relationship between N, K, and r in exponential and logistic growth Exponential: rN Logistics: rN x (k-N/K) dN/dt (the rate) is the greats when N is half the K value Density Dependent factors: Starvation, disease, competition, predation, emigration, parasitism, accumulation of wastes Density Independent Factors: act regardless of population density or size, such as natural disasters, severe weather, fires, floods Density independent and dependent factors may interact Reasons why N may fluctuate around K: Temporary overshoot and dip this is because of the time lag

Lecture 22
Reasons why humans have, until now, mostly avoided density-dependent regulation of N We havent reached our carrying capacity, better technology, modify our environment, agriculture, and increase the resources available on the land. Successfully out competing anything that is competing with us. Improvements in medical healthcare, decreasing death rates. How and why r of human populations varies regionally Different conditions and in different wealth and economic areas Relationship between increasing economic development and b, d, r, dN/dt, as predicted by the demographic transition model Over time more and more wealth, preindustrial-birth rates and death rates are high r is low, over time populations move into the transitional stage- decrease in death rates birth rates increase little r is at its maximum, industrial- death rates and birth rates decrease r starts to level and become zero, post industrial stage- populations should decrease Ecological community: an assemblage of populations that interact with each other, this looks at more than one species Critical factor: limited by a single critical factor Tolerance: many species have multidimensional tolerance limits Role-based definition of niche: what an organism does

Resource-based definition of niche: What an organism needs and thus, where it lives) Fundamental niche: where a species could potentially live pre interactive niche Realized niche: where a species actually lives, post interactive niche Competition: if two species are competing for the same resources, resources become limited Types of competition (exploitative versus interference competition, intraspecific versus interspecific) Exploitative (scramble), trying to use the resources up first known as interference, directly interacting with each other, trying to get the killed prey item. Either of these types of competition can result in competitive exclusion, or resource partitioning. Competitive exclusion: total overlap in the niches or resource requirements, then this is unstable and they cant coexist. Species become specialized so that they can exist with other species. Resource Partitioning: Why realized niches are often smaller than fundamental niches o Competition, and interactions with other species Major results and conclusion of Gauses Paramecium experiments o One species reaches the carrying capacity, and the other species loses Why competition sometimes results in competitive exclusion and other times results in resource partitioning: If the overlap is too great then specialization cannot help to rid competitive exclusion, and if the overlap is less than the different species can specialize and avoid competitive exclusion and coexist.