Population Genetics - Evolution Exam #3 PDF

★​ Population Genetics ○​ Hardy-Weinberg Equilibrium: a null model for population genetics that serves as a baseline against which we can compare real or hypothetical data to understand how the frequencies of traits might change in populations; that is, how evolution...

★​ Population Genetics ○​ Hardy-Weinberg Equilibrium: a null model for population genetics that serves as a baseline against which we can compare real or hypothetical data to understand how the frequencies of traits might change in populations; that is, how evolution operates ​ Allele frequencies stay the same over time ​ Formulated independently and by two different people at the same time ​ Following conditions must be met: ​ Large population size - helps minimize the effects of genetic drift, random changes in allele frequencies ​ No natural selection - can’t favor genotypes over others giving all individuals equal chances ​ No migration occurs (no gene flow) - individuals from other populations cannot introduce new alleles by migrating into the population ​ No mutations take place - new alleles cannot be introduced into the gene pool through mutations ​ Mating is random - individuals must choose mates completely by chance, not based on any specific traits ○​ Calculating allele and genotype frequencies ​ 𝑝 + 𝑞 = 1 - allele frequencies 2 2 ​ 𝑞 + 2𝑝𝑞 + 𝑝 = population - genotype frequencies ○​ Statistical errors ​ Type I error: the rejection of the null hypothesis when in fact it is true. This is an alpha (α) error. We will be choosing an acceptable probability of doing this at 5% (α = 0. 05) ​ Not in H-W equilibrium ​ Type II error: fail to reject “accept” null hypothesis when it is in fact false ​ In H-W equilibrium ​ ○​ Chi-square analyses 2 2 (𝑜𝑏𝑠𝑒𝑟𝑣𝑒𝑑−𝑒𝑥𝑝𝑒𝑐𝑡𝑒𝑑) ​ 𝑥 = Σ 𝑒𝑥𝑝𝑒𝑐𝑡𝑒𝑑 ​ Use the chi-square test to find whether populations are at H-W equilibrium ​ Helps compare observed and expected values to determine if the difference is due to chance ​ Degrees of freedom = number of classes being compared - number of alleles ​ Represents the values that are free to vary and is how we take into account our sample size 2 ​ 𝑥 < critical value = fail to reject null hypothesis and is in H-W equilibrium 2 ​ 𝑥 > critical value = reject null hypothesis and is not in H-W equilibrium ○​ Pleiotropic genes: one gene that influences multiple traits ○​ Polygenic traits: trait that is affected by many genes simultaneously ​ Ex: height, skin color, eye color, etc, ○​ Quantitative trait: trait that depends on the cumulative action of many genes and the environment ​ Ex: height and weight can be affected by diet, exposure to toxins, climate, socioeconomic status, physical activity, etc. ○​ Modes of selection ​ Directional selection: moves in one direction and favors one trait over another ​ Ex: giraffes with longer necks reach more food and reproduce more than those with shorter necks ​ Stabilizing selection: average and moderate traits are more likely to survive and reproduce ​ Ex: robins (bird) typically lay four eggs because larger clutches may result in malnourished chicks, while smaller clutches may result in no viable offspring ​ Disruptive selection: natural selection selects for two or more extreme phenotypes that each have specific advantages ​ Ex: Gray and gray/white rabbits are better able to blend with the rocky environment than white rabbits  ​ ★​ Species Concept and Speciation ○​ Three species concepts ​ Biological species concept: species are groups of actually or potentially interbreeding natural populations, that are reproductively isolated from other such groups ​ Pros: emphasizes the importance of reproductive isolation, provides a strong theoretical basis for understanding speciation mechanisms ​ Cons: doesn’t work with fossils and organisms that reproduce asexually, may not be practical for species that are geographically isolated ​ Morphological (Phenetic) species concept: species are clusters of phenotypically similar individuals or populations ​ Pros: focuses on physical traits, can be used to identify species from fossil records where reproductive behavior is unknown ​ Cons: doesn’t work on cryptic species, may not accurately reflect genetic diversity within a species, can be misleading due to convergent evolution ​ Phylogenetic species concept: species are the smallest monophyletic group that shares a unique derived character absent from all other groups in the phylogeny ​ Pros: can be applied to both extant and extinct species, provides a more detailed understanding of species relationships based on genetic data ​ Cons: requires extensive genetic data which can be challenging to obtain for many species, may lead to identification of very small distinct species lineage  ​ Evolutionarily independent lineages: groups of populations that have evolved separately from other species ○​ Cryptic species: species that are indistinguishable morphologically, but divergent in song, calls, odor, or other traits; traits that are important to reproductive isolation ​ Ex: Similar species of mouse lemur each have different calls ​ Similar species found in the same region tend to have different calls than another similar species found in another region ○​ Speciation: creates new species by splitting a population in two or more genetically independent lineages ​ Allopatric speciation: a process that occurs when a biological population becomes isolated from the rest of its species, preventing or limiting gene flow ​ Sympatric speciation: a process where a new species evolved from an ancestral species while both continue to live in the same geographic area ​ ○​ Mechanisms for evolutionary isolation ​ Allopatric model: a model of speciation where new species evolve due to geographic isolation ​ Geographic isolation: the physical separation of organisms or places by geographical barriers, such as mountains, oceans, or water forms ​ Dispersal model: population becomes divided into two or more geographically isolated parts because some individuals leave and found new populations ​ Vicariance model: populations become divided into two or more geographically isolated parts because some barrier arises, separating the once continuous population into pieces ​ The barriers can go away  ​ ​ Sympatric model: theoretical framework explaining how new species can arise within the same geographic area without physical barriers ​ This can occur when the population feeds on different types of food eventually leading to different species due to different food preferences and mating behavior, leading to reproductive isolation ​ Polyploidy: organism with two or more than two complete set of chromosomes ​ Polyploidy can affect sexual selection by potentially alerting an organism’s reproductive strategy, including the ability to self-fertilize and potentially leading to the evolution of new sexual traits due to the presence of duplicate genes ○​ Mechanisms of divergence ​ Genetic drift: a random process that causes the frequency of certain genes in a population to change over time ​ Bottleneck effect and founder effect ​ Natural selection: explains how organisms with traits that are better suited to their environment are more likely to survive and reproduce ​ Ex: Giraffes with longer necks are able to reach food while giraffe with shorter necks don’t reach a lot of food and don’t survive ​ Sexual selection: a type of natural selection that occurs when organisms compete for mates or access to a partner’s gametes ○​ Achievement of reproductive isolation ​ Allows populations to evolve independently, leading to the formation of new species (speciation) by preventing gene flow between species; can lead to distinct phenotypes and genetic variations; allows populations to  specialize in specific ecological niches, maximizing their fitness within the environment ○​ Hybridization: production of offspring by interbreeding between members of genetically distinct populations (different species) ​ The fate of hybrids depends on their fitness (how well they reproduce), especially relative to parent populations ​ Sometimes polyploidy results from hybridization ​ Ex: a mule is the product of a male donkey and a female horse ○​ Adaptive radiation: the divergence of a clade into populations adapted to many different ecological niches ​ Because of the conditions they are radiating into many other taxa ​ Each new species evolves to exploit a different nice such as food source ​ → beaks have adapted to different food sources available on the Hawaiian archipelago ★​ Evolution of Sex ○​ Sex vs. Gender ​ Sex refers to biological differences between males and females (chromosomes, hormones, and reproductive anatomy) ​ Gender refers to a person’s self representation as male or female ( self-identified and may change throughout a person’s life) ○​ Costs and benefits of asexual and sexual reproduction ​ Sexual reproduction ​ Costs: recombination can destroy positive allele combinations, energy and time cost in finding mates, risk of contracting diseases (STDs) or parasites, increased risk of predation including by potential mate, only 50% of your genes are passed on ​ Benefits: creates genetic diversity of within a population, disease resistance, and it facilitates natural selection allowing beneficial traits to be passed on ​ Asexual reproduction ​ Costs: there is no variation within the population making them susceptible to environmental changes or diseases that could affect  the entire population, any harmful mutations in the parent organisms will be passed onto the offspring, and rapid reproduction can lead to increased competition for food and space within the same environment ​ Benefits: rapid population growth which can be beneficial in colonizing new habitats, requires less energy because only one parent is needed, preserves beneficial traits, no need for a mate ○​ Parthenogenesis: reproduction from an unfertilized egg ​ A type of asexual reproduction ​ Females can reproduce even without a male to mate with ○​ Hypothesis for origin of sex ​ Parasitic DNA hypothesis: exchange genetic material that codes for its transmission and propagation ​ Sexual reproduction enhances the spread of parasitic genetic elements that code for doing this horizontal gene transfer ​ DNA repair hypothesis: diploids can repair damaged genetic material (DNA) via homologous recombination ○​ Adaptiveness of sex and hypothesis for maintenance of sex ​ Why is sex maintained? ​ Purge deleterious mutations: sex breaks apart harmful allele combinations by stopping the irreversible build of deleterious mutations in finite asexual populations (e.g. Muller’s ratchet) ​ Red queen hypothesis: sexual reproducers are more likely to create new genotypes that are able to adapt to environments that fluctuate, including exposure to parasites ​ Muller’s ratchet: a genetic process that occurs in asexual organisms when there is no recombination and that results in a buildup of harmful mutations ​ Linkage disequilibrium is increasing ​ Average fitness of whole populations declines over time, with natural selection increasing working against classes with high genetic load ​ Sex breaks the ratchet ​ Linkage equilibrium: a genetic condition where DNA sequences are far enough apart to be independent of each other ​ One of the purposes of sex is to maintain diversity, resynthesizing that diversity each generation in order to continually rebalance the genetic portfolio of the species ○​ Roles and functions of sex in organisms  ​ Generates a wider range of genetic combinations within a population enhancing the species ability to adapt to changing environments, allows for beneficial traits to be more readily passed onto future generations, gametes fuse during fertilization to form a zygote, one sex produces numerous small gametes (male) and the other sex produces fewer larger gametes (female), and complex behaviors that facilitate mate selection ★​ Sexual Selection ○​ Sexual dimorphism: a biological trait where males and females of a species have different physical characteristics, even if they aren’t directly related to reproduction ​ Ex: Male and female lion ○​ Intrasexual selection: process in which members of one sex (most often males) compete with each other for mating access to the other sex ​ Ex: Flies, elks, and moose have antlers to fight others ​ Sperm competition: competition between sperm of two or more males to fertilize a female’s egg(s) during sexual reproduction ​ Competition occurs when females have multiple potential mating partners ​ Alternative mating strategies ​ “Sneaking” tactics like letting a male call females while another male waits to mate with the female ​ Female mimicry to gain access to females without triggering aggression from other males ○​ Intersexual selection: process in which individuals of one sex select among individuals of the other sex as mates ​ Ex: frogs use mating calls to attract mates, fish perform courtship displays to attract mates, male peacocks with longer tails attract more mates ​ Direct benefits ​ Increased territory quality, increased parental care, and protection from predators ​ Good gene hypothesis: females ideally choose mates that have genetic advantages that increase offspring quality ​ Handicap principle: a hypothesis that explains how animals and humans communicate and signal reliably, despite the potential for deception and bluffing ○​ Ex: peacocks tails are long and heavy reducing it agility and making it more visible to predators yet they have an advantage and pass this trait on to future generations ​ Sexy son hypothesis: females ideally choose mates whose genes will produce male offspring with the best chance of reproductive success  ​ Males have the traits females like and use to choose ​ Cryptic female choice: a form of mate selection where females bias paternity towards certain males after mating ​ Females use behavioral, physiological, or morphological mechanisms to favor the sperm of one male over the other ​ Copulatory courtship: courtship behavior performed during or just after copulation to stimulate the female ○​ Signals used in cryptic female choice to influence what sperm will fertilize her eggs ○​ Sensory bias hypothesis: explains how female mating preferences evolve as a result of natural selection on sensory systems ​ Runaway sexual selection: an evolutionary mechanism that occurs when a secondary sexual trait in one sex becomes genetically linked to a preference for that trait in the other sex ​ Ex: a trait that is preferred by the opposite sex becomes exaggerated over generations that can be maladaptive or extravagant, but enhances an individual's attractiveness ​ Traits are appealing to the opposite sex but may be detrimental to survival can evolve