Bio 191 Exam 3

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Darwin & descent with modification:

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All organisms related through descent from common ancestor living in the distant past with the spread of descendents into different habitats and slow accumulation of modification (adaptations) through the mechanism of natural selection.

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Plato & typological view of nature:

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Plato’s view of 2 different worlds, the real world (invisible, unchanging, perfect and eternal where a single perfect Type for each species exists) and the illusionary world (perceived through the senses and imperfect and transitionary and the world where we reside).

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• Aristotle & “scale of nature” or great chain of being:

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Aristotle’s linear hierarchy from inanimate matter to plants, lower animals, human, to angels, and other spiritual beings to God.

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• Christian natural theology:

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Ray & Paley laid groundwork for comparative anatomy, physiology and the study of biological diversity; Paley’s watch and intelligent design that God designed everything with a specific purpose with species being the watch and God the watchmaker.

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• Linnaeus:

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binomial nomenclature and nested (hierarchical) classification system; grouped similar species into general categories, believed in Creator but classified humans with other primates

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Lamarck:

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1st theory of evolution: spontaneous generation, organ use and disuse (giraffes and their long necks) inheritance of acquired characters (giraffes and their long necks) and believed evolution occurred because organisms innate drive for complexity

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• Malthus:

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human suffering inescapable consequence of population’s potential to increase faster than food and other resources

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• Cuvier:

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paleontology who thought that each boundary in rock strata represented another catastrophe and mass extinction which led him to form the catastrophe theory

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• Hutton:

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gradualism which he based on geological features

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• Lyell:

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uniformitarianism which is the theory that Earth is shaped by ongoing and observable processes in small increments over a long period of time. Lyell incorporated gradualism into his theory. He was the first to date the Earth older than the Bible’s Genesis date.

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• Artificial selection versus natural selection:

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Artificial selection is the selective breeding of domesticated plants and animals by humans to produce certain characteristics which results in greater variation in traits (ex. dog breed). Natural selection is the different way that the environment modifies species in the same manner as A.S.

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• Five principles of Darwin’s theory of evolution by natural selection:

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competition (many more individuals are born than survive because resources are limited)
Variability (individuals vary in their characteristics), natural selection (some individuals are more successful in struggle to survive in a given environment than others), heritability (survivors pass on their characteristics to the next generation) and adaptation (unequal ability of individuals to survive and reproduce leads to gradual change in population, with favorable characteristics accumulating over generations)

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Problems with Darwin’s view of inheritance:

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blending inheritance was Darwin’s view that characteristics of an individual result from the blending of hereditary determinants from its parents. This idea was criticized for the flaw that blending inheritance would soon deplete the gene pool for variants that are necessary for natural selection. In response Darwin proposed pangenesis which incorporated the idea of blending inheritance and inheritance of acquired characteristics. The theory of Pangenesis was that of gemmules containing hereditary info in the gonads that were incorporated into reproductive cells. Inheritance of acquired characteristics was the source of variation in the Pangenesis Theory

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Weismann:

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Argued for the molecular distinction between soma (pheno) and germ plasm (geno) by cutting off the tails of mice and breeding them. Continuity of the germ plasm refutes inheritance of acquired characters

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Mendel:

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particulate theory of inheritance (individuals have two copies (alleles) of each hereditary factor or gene), law of segregation (each gamete receives one of two alleles present in the reproducing individual) and law of independent assortment (alleles from different genes transmitted to gametes independently of each other).

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Refining Mendel:

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multiple genes and continuous traits, incomplete dominance (two alleles both expressed in hetero which exhibit intermediate phenotype like red, white and pink snapdragons) and codominance(two alleles both expressed in the hetero which have a composite rather than blended phenotypes like blood types in humans)

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• Modern synthetic theory of evolution:

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Found that genetic variations arise by chance through mutation and recombination (crossing over of homo chromosomes during meiosis). They also found that populations evolve by changes in frequencies of alleles between generations resulting from genetic drift, gene flow, and natural selection. Also, speciation occurs gradually when populations are reproductively isolated like by a geographical barrier.

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• Definitions of evolution:

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Darwin- Descent with modification. Modern definition- change in the genetic composition of a population through time (across generations)

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Evidence for evolution:

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fossil record, homologies are the underlying similarities between structures with different functions in related species that come from common ancestor like that bones in the arms of humans, bats, and whales (anatomical, developmental & genetic) and vestigial traits are those structures that have marginal or no function in organism but resemble traits possessed by our ancestors such as a tailbone in humans, fingernails on manatee fins, appendix and wisdom teeth, and hip bones in boa constrictors.

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Factual evidence for evolution:

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–evolution in real time drug resistance in HIV (3TC drug interferes with reverse transcript of HIV RNA due to the 3TC molecules having a similar shape to the ctosine-bearing nucleotide which the HIV picks up instead of the DNA stopping the production of 3T cells but the resistant strain can discriminate between the drug and the DNA and so the resistant strain duplicates more quickly than if there were no 3TC drugs.
– industrial melanism in moths (Kettlewell’s experiments of peppered and melanic moths in post-industrial England)
– sickle cell anemia in African Americans (Sickle cell creates a malaria resistant but since there is so little malaria in America versus Africa, African Americans have a smaller chance of having the disease versus their African counterparts which still suffer from malaria. In Africa there is a 20% chance of being born with sickle cell and in America there is only a 4% chance.)
– antibiotic resistance in bacteria such as Mycobacterium tuberculosis (An extensive drug resisitant strain XDR-TB has developed allowing the disease to go from the brink of extinction in the 1950s to a new global epidemic I with 9 millinon new cases and 1.7 million deaths in 2004.)

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• Evolution as both theory and fact:

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It is undeniable that organisms evolve but the mechanism that causes this reaction is the center of the evolution debate.

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Popper’s principle of falsifiability:

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• the idea that in order for something to be a theory it must be capable of being disproved. .

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Population definitions

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• Population ( a group of individuals in a certain place capable of interbreeding), subpopulation (a locally interbreeding group within a geographic population, also called a deme or Mendelian population). Populations not individuals evolve, natural selection acts on individuals in a population which after time can result in the evolution of the population but individuals are only affected with mutations.

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Gene definitions

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• Gene pool (the sum total pf genetic info present in a population at any given point in time which consists of all alleles at all gene loci in all individuals of the population), genotype frequency (the relative proportion of a particular genotype represented by the number 0-1) and allele frequency(the relative proportion of an allele at a particular gene loci represented by the numbers 0-1. Calcualting the allele frequency allows us to quantify and better understand precisely what genetic variation is and how it works).

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Calculations

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• p = (NAA + 0.5NAa)/N and q = (NAa + 0.5Naa)/N; for two
alleles, p + q = 1
NAA+ NAa+ Naa= N = total number of individuals in a population
P= frequency of A
Q= frequency of a

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Hardy-Weinberg Theorem:

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• specifies the conditions that must be met in order for a population to remain at an equilibrium where no evolutionary change will occur.
– no mutation
– large population (no genetic drift)
– random mating (which will combine gametes at random to form genotypes)
– no gene flow (no migration)
– all genotypes survive and reproduce equally well (no selection)
– allele and genotype frequencies remain constant so that nAA = p2, nAa = 2 pq and naa = q2; p2 + 2pq + q2 = 1
* If given frequency of homozygous recessive genotype, be able to calculate all allele and genotype frequencies based on H-W Theorem*

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Agents of evolution:

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• mutation, genetic drift, non-random mating, gene flow and
selection (natural and sexual)

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• Mutation:

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any change in DNA sequence, from single base substitutions to deletion
or addition of tens or hundreds of bases, to duplication or reorganization of entire
chromosomes; ultimate source of genetic variation but usually low in rate

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Transposable elements:

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one category on non-coding DNA also known as mobile DNA, transposons, insertion sequences, or “jumping genes”. They are parasitic elements that accumulate by transposition (copying themselves to new locations in the genome). They can cause mutations by inserting into protein-coding genes and disrupting function or by inserting into regulatory sequences and increasing or decreasing protein production, or by moving segments of host DNA to new parts of the genome or by hindering precise chromosomal pairing during cell division resulting in chromosomal rearrangement. 45% of human genome is transposable element sequence

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• Horizontal transfer in bacteria:

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conjugation, transformation and transduction

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Traits acquired through horizontal transfer:

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new metabolic capacities,
virulence and antibiotic resistance

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Conjugative transposons:

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•conjugative transposons combine transposition with horizontal transfer. Allows for the antibiotic resistance in Clostridium difficile (the leading cause of hospital infections in the developed world).

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• Genetic drift:

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changes in allele frequencies due to chance; most important
in small populations. Bottleneck (sudden change in environment may drastically reduce population size resulting in change in allele frequency and potential loss of alleles) and founder effect (occurs when a new population is started by few members of an original population which can result in reduced genetic variations and disproportionate representation of rare alleles in a found population. Some examples are the high incidence of retinitis pigmentosa on Tristan de Cunha and Ellis-van Creveld syndrome among the Pennsylvania Amish.

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• Non-random mating:

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inbreeding (mating between close relatives which exposes lethal recessive alleles and usually depresses fitness and produces a deficit of heterozygotes and an excess of homozygotes), assortative mating (similar phenotypes mate preferentially with one another which increases homozygosity at some but not all loci) and disassortative mating (dissimilar phenotypes mate preferentially with one another which increases herterozygosity and might be important at the MHC loci.)

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• Non-random mating:

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inbreeding (mating between close relatives which exposes lethal recessive alleles and usually depresses fitness and produces a deficit of heterozygotes and an excess of homozygotes), assortative mating (similar phenotypes mate preferentially with one another which increases homozygosity at some but not all loci) and disassortative mating (dissimilar phenotypes mate preferentially with one another which increases herterozygosity and might be important at the MHC loci.)

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Gene flow:

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The movement of alleles from one population to another by migration, transport of gametes or immature stages by wind, animal, or water current, and the mating of individuals belonging to adjacent populations. It can oppose natural selection and reduce local adaptation especially in species with broad geographical range or when gametes or immature stages are transported from place to place.

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Selection:

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Natural selection- the superior survival and reproduction of some phenotypic variants compared to others under the environmental conditions that prevail at the time. Sexual selection- differential reproductive success resulting from competition between members of one sex, usually males, to achieve matings and/or fertilization (which can result in evolution of exaggerated male traits detrimental to survival.)

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Selection acts on phenotype of individual:

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through its physical traits, metabolism, physiology, and behavior. There are variations among individuals and certain traits enhance survival and reproduction in a given environment and those possessing such traits produce more surviving offspring and have a higher fitness (the contribution of an individual makes to the gene pool of the next generation relative to the contributions of other individuals) and indirectly adapts population to its environment by increasing or maintaining favorable genotypes in gene pool

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• Difference between natural selection and evolution:

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Natural selection occurs when different phenotypes vary in average reproductive success and is different from evolution by natural selection because natural selection will not produce evolutionary change in a population unless phenotypes differ in their genotypes (variation must have a genetic basis)

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What is different about natural selection as an evolutionary force:

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Natural selection produces adaptations (traits that increase ability of individuals to survive and reproduce in particular environment compared to individuals lacking the traits). Some evolutionary forces such as gene drift, gene flow, and mutation can cause maladaptation. Natural selection also causes allele frequency changes that proceed independently at different loci while genetic drift and gene flow tend to at act the same rate on all loci.

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Types of natural selection:

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Directional selection- one extreme phenotype is fittest. One ex is the colonization of a new environment by colonization of snady islands by dark deer mice and another ex. is environmental change such as survival of cliff swallows. Disruptive Selection-phenotypes at both ends of the range are fitter than the intermediates between them. One example is the beak length of black-bellied seedcrackers. Stabilizing Selection- the intermediate (average) phenotype is fittest. This is the most common type. One example is birth weight.

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Maintenance of genetic variation under selection:

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counters the removal of variation by directional and stabilizing selection. Heterozygote advantage- greater fitness of heterozygotes maintains two (or more) alleles at locus (ex is sickle cell maintained by malaria resistance). Varying selection (in time and space)- temporary oscillating selection favors one phenotype at one time, another phenotype at another time. Spatially varying selection favors one phenotype in one environment and a different phenotype in a second environment. Negative frequency dependent selection- the fitness of the phenotype depends on its frequency within population and ma favor more common phenotype (+) or more rare phenotype (-). Only negative frequency-dependent selection maintains variation.

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• Two mechanisms of sexual selection:

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: intrasexual competition (male-male competition involving the evolution of weapons or intimidating signals of strength and also where males compete to monopolize either females or a resource important to females such as harem polygyn or resource defense polygyny) and intersexual mate choice (female choice involving the evolution of sexually attractive traits and courtship behaviors)

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Sexually selected traits:

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weapons (stag antlers, tusks, horns in dnasty beetles) versus ornaments (peacock feathers, dewlap in lizards, stalked eyes of some flies, cock-of-the rock plumage)

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Sexual dimorphism:

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Marked differences between sexes in secondary sexual characteristics with greater dimorphism in polygynous species due to single males mates with many females which generates more intense sexual selection (ex. elephant seals)

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Why are males more often the target of sexual selection?:

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Males produce numerous,small and physiologically inexpensive sperm while females produce few, large, and physiologically expensive eggs. This limits the males reproductive success because he is limited by the number of females he can mate.

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Harem polygyny versus resource defense polygyny versus lek:

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Harem polygyny (guard females directly) like elephant seals and deer VS. resource defense polygyn like the Cortez damselfish VS Lek (female choice) which is the gathering of males to display to females like peacocks.

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Costs and potential benefits of female choice:

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Costs are time and energy spent looking for a mate and male harassment; benefits are material and genetic.

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• Sensory Exploitation:

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A potential benefit of the female choice. Males exploit pre-existing biases in the females sensory system to increase their attractiveness. This shows that female preference can exist before the male has acquired the trait.

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Good genes hypothesis:

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The hypothesis that sexually-selected traits signal heritable genetic quality and it uses the Handicap Principle that uses the example of a yellow-tailed bear.

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Distinctive features

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of human female (large breasts and butt and little body hair) and human male (V-shaped torso and manly face) evolved through mate choice

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Waist-to-hip ratio (WHR):

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the most extreme sexual dimorphism; male preference for low WHR (0.6-0.8) because narrow waists indicate non-pregenancy and therefore available to mate with.

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Female facial attractiveness:

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full lips, narrow chins, high cheekbones and large eyes. There is evidence that these traits indicate higher levels of pubertal estrogens and lower levels of androgen exposure.

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Male facial attractiveness:

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Correlated with the testosterone levels during puberty. Masculine faces are an honest sign of health and resistance to pathogens and parasites.

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• Short-term versus long-term female choice for male facial characteristics:

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trade-off between genetic quality and parental investment, a cute boy pre-cycle and a provider to have a baby with!

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Species definitions

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Speciation (the process by which one genetically-cohesive population splits into two or more reproductively isolated populations) as bridge between microevolution (evolution within the population) and macroevolution (evolution change above species level)

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Biological species concept and its limitations

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Biological species cannot be applied to asexual organisms, fossils, or organisms about which little is known regarding their reproduction.

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Morphological, paleontological and phylogenetic species concepts:

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Morphological is a when a species is defined on basis of being sufficiently morphologically distinct from all others and may involve multivariate stat tests of variation between species in relation to variation within species. Paleotological focuses on morphological discrete fossils known only from fossil record. Phylogenetic species concept is a group of animals that share a common ancestor with a lineage that maintains its integrity with respect to other lineages through both time and space and at some point in history members diverged from one another and when the divergence became sufficiently clear the populations are regarded as different species.

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• Stages in speciation process:

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1. Single reproductively-cohesive population, 2. Barrier to gene flow splits population into tow or more isolated populations, 3. Populations gradually diverge, 4. Reproductive isolating mechanisms evolve, 5. Members of populations incapable of interbreeding, 6. Populations become separate species.

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Geography of speciation:

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Allopatric (most common) is speciation in different homeland resulting from geographic separation of populations through vicariance and disperition with colonization. Parapatric speciation is speciation alongside resulting from the evolution of reproductive isolation between spatially adjacent populations resulting from environmental discontinuity. Sympatric speciation is speciation with single locality resulting from polyploidty in plant sand host shifts in insects.

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Allopatric speciation through vicariance:

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Involves emergence of geographic barrier (river or mountain range) that divides previously continuous populatins allowing the evolution of reproductive isolating mechanisms between populations that are geographically separate. One example of this are the Harris and White-tailed antelope squirrels at the Grand Canyon.

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Allopatric speciation through dispersal and colonization:

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Rare dispersal events results in colonization of isolated habitat (offshore islands) some example are Galapagos finches and Hawaiian Drosophila.

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What determines the tempo of allopatric speciation?:

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Mutation and genetic drift lead to slow allopatric speciation while natural and sexual selection lead to more rapid allopatric speciation. Sexual selection causes a rapid divergence in male sexually selected traits and female mating preference which accelerates the rate at which mating-stage reproductive isolation evolves

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• Secondary contact and reinforcement:

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Populations may come together again after isolation and if reproductive isolating methods are not complete than secondary contact may result in hybridization and possible reunification of the gene pools.

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Parapatric speciation:

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Speciation alongside (evolution of reproductive isolation between spatially adjacent populations that have limited gene exchange and occurs in absence of an obvious geographic barrier). May occur when a sharp environmental discontinuity develops within the range of species. An ex. is plants growing on mine tailings flower at different times than plants in surrounding pastures in Wales.

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• Sympatric speciation:

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Speciation in the same homeland with the development of reproductive isolation with geographical barriers such as in flowering plants via polyploidy (multiplication of the number of chromosome sets) and autoploidy (duplication of chromosome set of a single species). Polyploidy individuals cannot interbreed successfully with members of either parental species because polyploidy individuals have twice as many chromosome sets than their parents. Autoploidy can result in nearly instantaneous speciation.

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Polyploid in animals

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In animals, host plant shifts resulting in sub-populations with assortative mating may be a common cause of sympatric speciation in phytophagous insects. Apple maggot fly as example of sympatric speciation in animals

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• Prezygotic reproductive isolating mechanisms:

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mechanisms that impede mating between species or hinder fertilization of ova if members of different species do mate. Pre mating examples are habitat, behavioral or temporal isolation. Post mating examples are mechanical or gametic isolations.

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Postzygotic reproductive isolating mechanisms:

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Mechanisms that act to reduce the viability of fertility or fertility of hybrid. It reduces hybrid viability by an incompatibility between geonomically-imprinted, nuclear genes (ex. deer mouse hybrids) and nuclear/mitochondrial incompatibility. Reduced hybrid fertility causes meiotic disruption (ex. mules). Hybrid breakdown is when the F1 hybrid is viable and fertile but subsequent generations are invariable or infertile (ex. Drosophila)

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Haldane’s rule (of speciation):

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In hybrids produced by interpopulation or interspecies crosses, the heterogametic sex is more likely to be inviable or infertile. In mammals and insect males are heterogametic, in birds and Lepidoptera females are heterogametic.

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• Taxonomy:

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the theory practice and rules of classifying organisms based on similarities between species.

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Domain, Kingdom, Phylum, Class, Order, Family, Genus and Species (Do Kings Play Chess On Fiber Glass Stools?)

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Domain, Kingdom, Phylum, Class, Order, Family, Genus and Species (Do Kings Play Chess On Fiber Glass Stools?)

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Systematics:

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the scientific study of biological diversity and evolutionary relationships aong organisms both extinct and modern. Will Hennig thought that he grouping should reflect evolutionary relationships.

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Evolutionary systematics versus phenetics versus cladistics:

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Evolutionary is classification based on combo of common ancestry and overall phenotypic similarity. Phenetics is classification based on overall phenotypic similarity and uses a multivariate statistical method where all traits are given equal weight. Does not distinguish between primitive and derived traits. Cladistics is classification based strictly on the recency of common ancestry. Considered the proper approach to taxonomy.

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Monophyletic group versus paraphyletic group:

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Paraphyletic groups have a common anscentor and some but not all descendants. (Ex. lizards and dinos) Monophyletic groups identified by shared traits.

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Limitations and uses of fossils in phylogenetic reconstruction:

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In principle, fossils provide direct evidence of evolutionary transitions but in practice, the data is too fragmentary. Fossils are useful for designating outgroups and estimating divergence time of taxa.

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• Limitations and uses of comparative studies of development in phylogenetic reconstruction:

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Structures in early developmental stages may show evolutionary relationships not evident in adults. Seen in frog embryos and sea squirt larvae.

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Von Baer and Haeckel's Law

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Von Baer’s law (common to a higher-level taxon and often appear in development before characters unique to lower-level taxon, class to order, such that all embryos possess gill slits and tails) and Haeckel’s law (The development of the individual organism repeats the principle stages of the evolutionary history of a species or lineage, ontogeny recapitulates phylogeny)

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• Paedomorphic species and violations of Haeckel’s law:

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Some species retain juvinelle traits through adulthood which means that Haeckel’s law cannot be an applicable method for phyloeny reconstruction.

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What is a character-state matrix?:

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The distribution of character states in a set of organisms provides info on evolutionary relationships (ex. jaws, lungs, hair).

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Shared, derived characters versus shared, primitive characters:

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Shared, derived is an evolutionary novelty unique to a particular lineage and not shared by common ancestors and provides the basic cladistic classification. Shared, primitive is a character state shared beyond the taxon and shared by common ancestors and provides no info on evolution.

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Outgroup:

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Monophyletic groups can be identified by shared, derived characteristics. Outgroup is a taxon that diverged earlier than the ingroup. Comparing each outgroup to ingroup differentiates between shared, derived and shared, primitive characteristics while assuming that those shared by outgroup and ingroup must be primitive and predates the divergence of the groups.

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Principle of parsimony as:

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Parisomy is the principle of the evolutionary tree with the fewest events occurring and minimizes the total number of character state changes.

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Phenotypic versus gene and genomic characters in phylogeny reconstruction:

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P: morphological, physiological and behavioral. G: nucleic acid sequence (DNA or RNA), gene order, genome

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Advantages of molecular characters:

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No environmental effects, can evolve in clock-like fashion, DNA is ubiquitous to life and homo sequences exist among all taxa, protein-coding provides model of evolutionary change, and different genomic regions evolve at different rates and can therefore be used for phylogenetic questions at different hierarchical levels.

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• What are slowly-evolving gene regions good for?:

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Reveals that prokaryotes are composed of Bacteria and Archaea groups and also indicates that Archaea share more recent common ancestor with Eukarya than with Bacteria.

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What are rapidly-evolving gene regions good for?

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Useful for fine-scale phylogenetic resolution at levels of populations, species, and genera. Also good for mitochondrial genes

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• Disadvantages of molecular characters:

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cost, convergence and saturation

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Why is systematics important?:

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For testing evolutionary hypotheses, for finding the origins of human disease, and in forensic applications (forensic phylogenetic systematics)