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56 Cards in this Set

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What is "essentialism?" (included in doctrines before darwin) and what were the views in the natural history before Darwin?
1)Typological (study or systematic classification of types that have characteristics or traits in common) views of the diversity of life.
2) a. world and its components as unchanging. b. variation as unimportant, accidental, undesirable (looking for the "ideal brown bear") c. focus on characterizing the IDEAL type of each species, and the realtions among these ideal types.
Define Evolution.
A gradual process of change or development. Early evolutionary ideas not necessarily evolution of natural selection->there were other pre-darwinian evolutionary ideas.
An example of someone involved in Early Evolutionary Ideas is Jean Baptiste Lamarck (1744-1829)-Zoological Philosophy, 1809. Explain his ideas.
Linear progression, ea species on its own. a. New "species" created spontaneously as simple and primitive. b. Inheritance of acquired characters. c. Each species then progresses toward more complex and perfect forms of life (during their lifetime).
An example of someone involved in Early Evolutionary Ideas is Sir Charles Lyell (1797-1875)-Principles of Geology, 1830. Explain his ideas.
Uniformitarianism-the current features of the world result not from catastrophic events but instead from the gradual effects of currently obervable processes acting over vast periods of time. E.g., Geological features result from erosion, sediment deposition, etc, rather than from a few catastrophic events such as the Great Flood.
What were the two major questions posed by Charles Darwin (1809-1882) in trying to understand life on the planet?
1)Diversity of living forms-where did they come from, what's the process?
2)"Fit" or adaptedness to environment-why, how?
In order to recieve a concept such as lyell's, must make a leap in ideas as Darwin did. What was Darwin's insight on his first question on the existence of species and where did he get it?
1)All living organisms descended from a common ancestor and diversified into the man species now observed.
2) Darwin saw evolution as a branching process rather than a linearly progressing one=>like the galapagos mockingbirds of similar species, similar b/c they share a common ancestor. We represent this branching with a "phylogeny," a geneology of populations showing the evolutionary relationships among organisms. Branch tips can be populations, species, families (of many species), etc. Nodes are splitting events. If branch tips are species, nodes indicate speciation.
What was Darwin's insight on organisms' fitness/adaptedness to their surroundings?
Organisms evolved to fit their environments. Instead of Lamarck's idea of inherited evolved characteristics (which evidence didnt really support, think of the lifting-weights-problems), he explained it by the Transformational Process [evolutionary process in which the properties of the ensemble change over time b/c ea individual component of the ensemble changes over time-"transformers or flowers." In regards to resistance to antibiotics, it happens little by little-but we know this doesnt happen.] and Variational Processes [evolutionary process in which the properties of the ensemble change over time due to some process of sorting among the individual (and possibly unchanging) components. the change occurs b/c something did the sorting. ex: bonsai trees,sifting soil, rocks out. In regards to antibiotic resistance, the variation already exists in the population (more or less sensitive) which goes to one particular by and outside sorting.]. Darwin's Second Idea was that Organisms evolved to fit their environments by the variational process of natural selection. Variation acts as a fuel, not just a side occurence.
Explain what Darwin's Evolution by Natural Selection needed.
[crows act as filter=>eat green beetles and eventually only orange beetles are left]
1)Variation among individual (req'd in order to have something to sort on)
2)Heritability of Traits(time needed, things can't be muddled)
3)More offspring are prduced than can survive(to continue to sort)
4)Differential survival by trait(fitness-orange beetles more able/fit to survive than green).
What were three of the deeper problems that Darwin faced?
1)How is variation preserved? a. Blending inheritance-tall parent and short parent=>everything becomes neutral just from reproduction. b. Effect of natural selection-that gets rid of variation too! How would variation survive to drive on natural selection?
2)How do complex structures evolve? E.g., evolution of the eye..correctional abilities,etc. how does natural selection play in complex processes, etc?
3)Why are species so discrete? Absence of intermediate forms(macroevolution). If natural selection is a gradual modification, wht are there lions and tigers and bears?, including in fossil evidence?
What questions was Mendedl trying to answer and which H's did he junk?
1)What are the basic patterns of inheritance?
2)Blending inheritance (everyone believed in it) and Inheritance of acquired characters(contrast idea believed, it's a transformational idea).
What did Mendel use as a model organism and what were the two main topics he studied with them?
A. Heritable Variation-1.studied 7 characteristics: 2 types/variants of each. 2.pure breeding (or true breeding)lines available-a.purple-flowered parent(s)=>always had purple offspring. b.white-flowered parent(s)=>same as above.
B. Breeding System-
1.Self-ferilization is normal
2.Mendel could arrange crosses by cutting anthers and performing hybrid=a mix of two types by hand pollenation.
With regards to Mendel's anaylization of the inheritance of a single trait, what was the first of his experiments of the 7 traits and how did it work out? [mass experiment subjects needed, thnk "white man cant jump"]
A. Flower color: purple x white
1.parentals crossed to yield F1(first filial) offspring, then F1s selfed to yield F2 generation.
2.Results-
a.Phenotypes of F1s: all purple (A BOTHER TO THE THEORY OF BLENDED HERITANCE IDEA).
b.Ratio of purple:white in F2: 3:1 still a contradiction to past beliefs, not excluding that the white disappeared and then reappeared.
B. Reciprocal crosses identical-doesnt depend on the sex of parent.
C. The other six traits gave similar results-so that he could say that it was a general property of traits in peas at least, not only color.
Name and explain the four portions of Mendel's Model.
1)Inheritance is Particulate: not blending.."genes act like particles."
2)Each Individual pea plant has two alleles, or versions, of each gene:-an allele for purple and one for white->still the same gene. a. A gene is a "hereditary factor"=something that influences a particular trait and is transmitted to gametes and thus to offspring. "gamete"=a reproductive cell that combines with another gamete to form an offspring (sperm/egg). b. individuals can be: homozygous-2 of same allele or heterozygous-2 different alleles.
3) Some Alleles are Dominant to Others; Some Alleles are recessive: a. dominance/recessiveness is defined only in terms of the appearance of heterozygotes=>1 trait (dominant) is seen.
b.genotype(listing of the alleles present) and phenotype are distinct. notation: uppercase italicized letters for dominant alleles.
c.genotypes may be: PP-homozygous dominant, Pp-heterozygous, pp-homozygous recessive.
4)During Gamete Formation in a Parent, Pairs of Alleles Segregate into Different Gametes: ea gamete contains 1 allele of each gene-"principle of segregation."
5)Male and Female Gametes Fuse to Form a Zygote=>cell thats a product of gamete fusion)offspring: each offspring has 2 alleles, one from each parent.
In interpreting the monohybrid cross (mendel), where PP father(purple) x pp mother(white): F1s genotype and phenotype (thy selfed) are:...? AND what does the punnett square predict that the frequency of each genotype is in F2 offspring?
1)heterozygous=>phenotype: purple--Pp.
2)1:2:1 genotype prediction which is what he saw, worked for all 7 traits. 3:1 phenotypes.
In analyzing the inheritance of two traits (via dihybrid cross) Mendel's question was:are the alleles for different genes transmitted together or independently? The experimental cross was: Yellow-round seeds(YYRR) x green-wrinkled seeds(yyrr)=>pure-line genotypes. H1 was:alleles from different genes are transmitted together. H2 was:alleles from different genes are transmitted independently.
Assuming H1, predict the results of the cross.
Assuming H2, predict the results of the cross.
1)Parental genotypes:YRYR yryr
Gametes produced: YR yr
F1 offspring from cross: YRyr.
Gametes produced by F1 parents: YR , yr.
F2 offspring from selfing(by punnett square):YRYR, YRyr, yrYR, yryr.
Ratio of F2 phenotypes: 3:1 (yellow-round:green-wrinkled)

2)Parental genotypes: YYRR, yyrr.
Gametes produced: YR , yr
F1 offspring from cross: YRyr
Gametes produced by F1 parents: YR, yR, Yr, yr.
Ratio of F2 phenotypes: 9:3:3:1 (yellow-round:green-round:yellow-wrinkled:green-wrinkled).
Explain the actual results of Mendel's YYRR x yyrr crosses.
F1s are yellow-round seeds. When F1s are self-fertilized, phenotypes of F2 offspring are: yellow-round:315, green-round:108, yellow-wrinkled:101, green-wrinkled:32. The ratio of observed phenotypes therefore is 9:3:3:1, which supports the H2 hypothesis. Mendel's conclusion: Principle of Independent Assortment: 1865. (*note: not always true->many genes dont behave this way.).
The physical basis for Mendel's Rules involved: ..?
Mitosis and Meiosis.
Mendel's work on heredity provided two main lessons about variation:...?
1)Genes dont blend, so variation does not disappear when alleles are "mixed" in offspring.
2)A sense of what variation actually is: Genetic variation exists in a population when there is more than one allele for a given gene.
What is the ploidy concept?
haploid: one of ea type.
diploid: two of ea type.
n notation:used to talk about #s of types.
components: chromosomes, chromatids, centromere.
What is Mitosis and its basic as well as in-depth processes? What are the consequences of Mitosis?
1)the process of cell division used for growth in multicellular organisms, and for reproduction in most asexual eukaryotes.
2)Each cell has a number of thread-like chromosomes. In eukaryotic cells, these are found in the nucleus. These chromosomes come in different types, typically with two of each type in ea eukaryotic cell (ex: long & short).
3)Mitosis[n=2,2n=4): 1.Interphase (pre-mitosis):chromosomes and centrosomes(outside of nucleus) replicate. 2.Prophase/Prometaphase:chromosomes condense, mitotic spindle begins to form (moves 'round the chromosomes), Nuclear envelope breaks down, spindle fibers (made of microtubules)contact chromosomes at kinetochore.
3.Metaphase:chromosomes complete migration to middle of cell (along metaphase plate).
4.Anaphase:sister chromatids separate, chromosomes pulled to opposite poles of the cell.
5.Telophase:nuclear envelop re-forms, and the spindle apparatus disintegrates.
6.Cytokinesis (post-mitosis):cytoplasm is divided, cell division->2 daughter cells form.

4)Ploidy stays the same, chromosomes identical to those in parent.
What is Meiosis and its basic as well as in-depth processes? What are the consequences of Meiosis?
1)type of cell division used when producing gametes (sex cells).
2)Two phases:
a. MeiosisI: Reduces the ploidy, diploid goes to haploid, which is necessary b/c of gametic fusion that occurs in fertilization.
b.MeiosisII: sister chromatids separate as in mitosis.

3)MeiosisI [n=2, 2n=4]:
1.Interphase(pre-meiosis):chromosomes and centrosomes replicate in parent cell, in uncondensed state.
2.ProphaseI:chromosomes condense, nuclear envelope breaks up, spindle apparatus forms. synapsis of homologous chromosomes (tetrad-4chromatids from homologous chromosomes)(chromosomes like one another come together and cross-over).
3.MetaphaseI:Pairs of homologs(tetrads) to middle (metaphase plate).
4.AnaphaseI:Homologs separate and begin moving to opp. poles (still have sister chromatids), distributed evenly.
5.TelophaseI and Cytokinesis:Chromosomes move to opp. sides of cell, then cell divides.

MeiosisII:
6.ProphaseII:centrosomes replicate, spindle apparatus forms.
7.MetaphseII:chromosomes line up along metaphase plate.
8.AnaphaseII:sister chromatids separate, begin moving to opp. poles.
9.TelophaseII and Cytokinesis: chromosomes move to opp. sides of cell, then cell division.

4)ploidy gets halved, chromosomes:4daughter haploid cells, synapsis made them all different.
chromatin=..?
the material that makes up eukaryotic chromosomes: a DNA molecule complexed with histone proteins. can be highly compact (heterochromatin) or filamentous(euchromatin).
List four examples of evolution.
1)antibiotic resistence
2)HIV evolution: antiviral resistence
3)artificial selection-extremely influencial to darwin.
4)industrial melanism-peppered moth
5)darwin's finches-less examples of natural selection w/o human intervention b/c there's less to observe.
Contemporary evidence for darwin's idea: all living organisms descended from a common ancestor and diversified into the many species now observed...?
1)similarities among living organisms: homology(shared characteristics resulting from common descent),not analogy.Ex of homology:
1.structual
2.universal genetic code(yeast and mouse can use ea other's genes)
3.genetic(consistent use, etc)
4.developmental(embryotic)
5.biochemical(shared bc shared by common ancestors)

2)The fossil record-things should be found in order, progression/evolution to date.
3)Vestigial structures:characters that have traits that are 'relics' of their ancestry. ex:whale's pelvic bone pointing to it having been a tetrapod., snake's femurs.
Contemporary evidence for darwin' idea "organisms evolved to fit their environments by the variational process of natural selection."...?
1)Fit of organisms to environment.
2)Evolution in 'real time';breeding, antibiotic resistence industrial melanism.
3)Convergent evolution:armadillos, ant-eaters, spiny ant-eater-dont have common ancestors but common problems that led to similar solns.
What is mutation, its problems and solution?
1)change in the heredity material of an organism. it is random and undirected, the sorting process prospers the surviving one in natural selection.It is the ultimate source of all genetic variation.
2)Inevitable error in copying makes it hard to maintain traits b/c it involves copying error., prob most seen in viruses or copies of paper in generations.
3)strong selection(full answer for bacterial).
With regards to the evolution of a complex structure, how can natural selection act as a creative force instead of merely a mechanism for refining phenotypes? lungs from gills? language?
"from biplane to jet"-tinker a bit at a time-ea time part is changed, the bi flown. point being , ea one has to yet perform fairly well for allowing process to continue. consider the vertebrae eye.
Fitness=?
Ability of an organism to produce surviving offspring (relative to others in the population).
Adaptation=?
Any heritable character that makes an organism more fit in its abiotic and biotic environment.
Name the four major constraints on adaptation.
1)mechanical
2)tradeoffs
3)coevolutionary arms race
4)myopia: natural selection cant plan ahead.
Which aspect of meiosis explains mendel's principle of segregation?
the separation of homologs during meiosisI.
With regards to the sources of genetic variation and the chromosome theory of inheritance, give the 3 propositions.
1)genes are found on chromosomes. (initial idea-"beads on a string"
2)the principle of segregation results from the separation of homologous chromosomes at meiosisI-fig 13.9a
3)the priniciple of independent assortment occurs b/c maternal and paternal homologues assort independently at meiosis I -fig 13.9 b.
With regards to the sources of genetic variation and the sex linkage theory, give over its four portions.
1)Fruit flies as a model organism

2)Discovery of white-eye mutants(an individual w/ a new trait. mutation=a novel trait-new phenotype): Red-eyed female x white-eyed male. White-eyed female x red-eyed male. Reciprocal crosses give different results..what the heck is going on? for mendel, there was no difference!

3)The discovery of sex chromosomes: Nettie Stevens(grasshoppers). XY sex determination: X and Y act like homologs, @ meiosis (they synapse) but different structures, diff genes. Autosome=a non-sex chromosome.

4)Hypothesis: W as an X-linked trait(on the x chromosomes).
a. Write X-linked traits as: x^W =>x=sex allele, W=normal/red, w=white [w is sex-linked and x-linked]. sexlinkage=found on a sex chromosome.
b. Predicting the outcomes of crosses involving X-linked traits if X-linkage explains the data, then the chromosome theory of inheritance is supported.

Red-eyed females x white-eyed males
parental genotypes: x^Wx^W, x^wY
Gametes produced: x^W, x^w,Y
Punnett square(predict genotypes and phenotypes of F1 offspring).
Offspring Genotypes:x^Wx^w, x^WY
Offspring Phenotypes: female-allred, male-all red.

White-eyed females x red-eyed males

Parental genotypes:x^wx^w, x^WY
Gametes produced:x^w, x^W,Y
Punnett square.
Offspring genotypes:x^wx^W, x^wY
Offspring phenotypes:female-allred, male-allwhite.
With regards to the sources of genetic variation and Linkage, recombination, and linkage mapping, give over the two ideas.
1)Morgan's lab found a series of genes on the X chromosome; inheritance pattern like white ebony body, yellow body, brown eye.

2)Crosses with linked genes (genes that are located on the same chromosome): difference b/w linkage(on the same chromosomes) and sex-linkage? eg, white and yellow are linked, sex-linked and x-linked:
a. Prediction: linked genes should violate Mendel's principle of independent assortment. x^Y=normal color, x^y=yellow body, linked genes that are also sex-linked x^WY.
Morgan's experimental test of the linkage prediction: homozygous white-eyed, normal-bodied female x red-eyed, yellow-bodied male.
Parentals: x^wYx^wY, x^WyY
F1 females:x^wYx^Wy
F1 males:x^wYY

let F1s mate.
genotypes of the "weird" males: x^wyY, x^WYY

crossing over as an explanation: mustve happened somewhere b/w them=>recombination (=generation of a new combinatoin of alleles along a chromosome, a result of crossing over).

Summarization of sources of genetic variation:
1. Mutation introduces new alleles
2. Independent assortment of maternal and paternal chromosomes. gametes have a random assortment of alleles from mom and dad.
3. Crossing over (routinely occurs multiple times along the length of ea chromosome):produces new combinations of alleles along ea chromosome ex:blond, straight hair.
4. Outcrossing=combine haploid genomes from different parents to form diploid offspring. potentially, new combinations of alleles at ea gene.
Population genetics allow us to model what and requires shifting our perspective of what?
1)what happens to allele frequencies and to genetic variation over evolutionary time.
2)from individual-based thinking to population-based thinking.
What is the Hardy-Weinberg Equilibrium and what does it require?
1)A null model in population genetics-what happens (pattern) if nuthin is happening(process).
2)Take a very simple population:
1.no natural selection
2.random mating
3.no mutation
4.no migration
5.large population size

the basic question:how do allele freq's and genotype freq change over time?

Creating a model:2 alleles, 1 locus.

Genotype: AA Aa aa
Frequency: x y z

where x+y+z=1

Allele frequencies are
Freq.[A]=2x+y/2
Freq.[a]=2z+y/2

Finding the next generation:
Genotype: AA Aa aa
Frequency: x y z

All possible matings:the crosses and their frequencies, writing out Punnett squares for ea mating..

The "Gene Pool" metaphor:
If the h-w conditions are met, we can use a "gene pool" approach instead.
1.imagine that all individuals contribute to a "gamete pool."
2.the next generation is formed by drawing gametes at random from this pool.

Calculations:

Parents: AA Aa aa
x y z

Allele freq. A a
(2x+y)/2 (2z+y)/2
Call these p q=1-p
Gamete pool A a
Gamete freq p q
Offspring AA Aa aa
genotypefreq p^2 2pq q^2
What are the Hardy-Weinberg Results?
1)Hardy-Weinberg genotype frequencies are
AA Aa aa
p^2 2pq q^2

2)Under H-W assumptions, allele freqs dont change from one generation to the next.

When various HW conditions are violated, ea of these becomes possible:
a. no natural selection: ex, AA lethal
Aa lethal
b. random mating: ex, sexual selection, assortative mating

3)No mutation:A->a, a->A will change frequency.

4)No migration:will change allele frequency.

5)Large Population-no genetic drift.
Explain: Neutral locus, Genetic drift, Genetic bottleneck.
1)Unselected genetic locus at which alternative alleles have identical fitness.
2)Random change in allele freqs due to sampling (sampling matters more w/ smaller samples-thus drift becomes more important).
3)reduction in population size, causing significant genetic drift.
B/c of genetic drift, a small population will tend to have less or more (by chance) genetic variation?
less. think of class sampling w/ males and females.
Sex helps perserve variation, but raises its own evolutionary puzzles. What is sex(in multicellular diploid eukaryotes)?
It involves:
1)Gametic fusion: production of diploid offspring via meiotic division followed by fusion of haploid gametes.
2)Outcrossing: gametic exchange b/w unrelated individuals.
3)Recombination: produces new chromosomal types by crossover b/w homologous chromosomes.
Why is sex surprising?
The two-fold cost of sex. (John Maynard Smith):

Individual level:a female passes on half as many copies of her genes if she reproduces sexually as she would if she reproduces asexually.

Population Level: A population of all females grows twice as fast as a population w/ both males and females.


Other problems w/ sex:
1)need to find (&impress) a mate.
2)Breaks up coadapted or locally adapted genes.Ex:two loci control teeth and temperment.
What are the advantages of sex?
1)Accelerates adaptive evolution.
2)Purges "deleterious mutation(any mutation that reduces an individual's darwinian fitness)" (muller's ratchet).
3)Red Queen hypothesis: dealing with parasites. "run as fast as you can to stay in the same place."
Adaptation is constrained-but evolution has ways around the constraints. So how can you go from biplane to jet?
1)Some path exists, and given enough time, evolution can find it. -multidimensional mountains in the fitness landscape which might provide a path.

2)Exaptation: a trait that evolved for one purpose(or w/o a purpose)but later came to served a different useful function. Ex:the evolution of wings. they prob served for many purposes.
What is the tree of life?
A hypothesis about evolutionary history and pattern on the largest of scales. A phylogenetic diagram indicating evolutionary relationships of all living organisms.
Linnaeus still worked really well b/c he had good intuition about what differences and similarities were more important, which tended to correspond closely w/ the idea of history and geneology.
Explain "taxonomy" and the ways it has been expressed/utilized.
1)naming and classification of species and groups of species.
2)Carl Linnaeus (1735): based on morphological similarity; typological view of species. "latin binomal" (Genus, species) naming system.

Post-Darwinian shift in classification: taxonomy reflects phylogeny:morphological and genetic data (historical).
The tree of life also sets the scene for Darwin's third problem (why does the tree look like it does, and why in particular are species on the trees so distinct if evolution is gradual?). What is the partial solution to Darwin's problem?
Sexual species are discrete b/c gene flow "holds them together."
What is a species according to the Morphospecies concept?
A morphologically discrete group of organisms separated from other organisms by a significant phenotypic gap.
What is a species according to the Biological species concept?
A population or set of populations whose members can potentially interbreed to produce viable fertile offspring.
Asexual species. Species concept cant be based on reproductive isolation. Why are asexual species discrete at all?
1)possibility: b/c then intermediates would fall into fitness valleys.
2)just reflects phylogenetic history.
What is a species according to the Phylogenetic species concept?
Each species is a group of phylogenetically close relatives. But how deep to draw the line?
What is a species according to the Ecological species concept?
Largest group of phylogenetically related individuals competing for the same ecological niche.
Speciation and extinction are the processes that give rise to the pattern in the tree of life. Explain speciation and the two different viewpoints.
1)speciation is the formation of two or more species from one ancestoral group, by isolation and divergence (genetically and morphologically). think island and river-split.

2)Allopatric speciation: Physical (geographic) barriers prevent interbreeding. Populations then diverge by selection and drift.

Sympatric speciation: speciation w/o geographical separation. Isolating barriers: host shift, polyploidy, behavior.

species then evolve isolating mechanisms which prevent gene flow across the species boundary. these may be selected or otherwise.
Are the rates of speciation differences or lengths a property of the niches? or a property of genetics?
we still dont know
What is "adaptive radiation?"
Rapid burst of speciation due to:

1. Evolutionary innovations[ecological opportunity, morphological innovation]. ex:exoskeleton, jointed limbs, flight.

2. Extinction of competitors, particularly during mass extinction.
Elaborate on Rates of extinction.
It is a continuous process, always occuring at some background rate due to chance and natural selection. It is accelerated by environmental change. Can occur in rapid bursts, known as 'mass extinction events.'
What determines the rate of macroevolution?
Balance b/w rates of speciation and extinction.