Biol 401 Quiz 1

Muslim Scholars ideas of evolution

hierarchies of complexity, temporal transitions between levels, species were not fixed could evolve

elizabethan evolution

“great chain of being”, species “fixed” through time

Carl Linnaeus

father of modern taxonomy, important in organization

Georges Cuvier

fossils resemble but are not the same as modern species, many past species extinct,

Cuvier discovered that

species are immutable (fixed), but the absence of necessary conditions results in extinction - thus number of species declining

Lamarck

life driven from simple to complex, adaptation occurs through inheritance of acquired changes

Philosophie Zoologique

advocated mutability of species, over generations organisms could proceed from one step to the next (did not discuss driving forces)

Limitations of Lamarck

evolution as striving, did not understand inheritance or natural selection

Lamarckian transformation

"internal force” something that changes the offspring during the lifetime of the organisms, inheritance of “acquired” characters

Charles Lyell introduced ideas that

extinction is permanent, species could not re-evolve as Lamarck proposed; and Uniformitarianism: the processes (erosion, volcanoes,…) responsible for the past (unobserved) events are still active and observable

Uniformitarianism happens as

gradual changes over time, (creek vs river, same thing just longer)

Thomas Malthus population growth

the principles of population growth and limited resources → under exponential population growth not everyone can survive

Charles Darwin voyage of the Beagle

found fossil deposits 7000 ft above ground, confirmed uniformitarianism; the earth is old

Alfred Russel Wallace

while sick he had a realization about the importance of competition and limited resources, independently developed the theory of evolution by natural selection

Wallace prompted Darwin

to go public, letters proposed similar evolutionary ideas; common ancestry and natural selection

preliminary facts of natural selection

species have high fertility, population size ~ constant, limited resources

preliminary inferences of natural selection

struggle for existence and fittest most likely to survive

further facts of natural selection

variation is ubiquitous and heritable; knew inheritance worked but not sure how

final inference of natural selection

natural selection leads to evolution

the struggle for existence from limited resources =

favourable variations tend to be preserved and unfavourable ones tend to be destroyed

cycle of natural selection

phenotypic variation → differential survival/mating success → reproduction and inheritance

reaction to Darwin

evolution was accepted (species were not fixed in time), natural selection was rejected because it lacked a satisfactory theory of inheritance

Blending mechanism of inheritance

“particles” of inheritance explain transmission of traits from parents to offspring

blending inheritance: parental body parts produces

“gemmules”, which move to sex organs and are passed on during reproduction, strength and number of gemmules determined the characteristic of the offspring

Gradualism

Darwin theorised small changes from one generation to the next, changes large enough to result in the formation of new species must occur during long periods of time

Mendel” “law of segregation” and “law of independent assortment”

no blending, basis of all modern genetics, first published in 1865 but remained unnoticed for many years, led to revival of Darwin’s theory

Hugo de Vries

rediscovered Mendel’s work when finding evidence that genetic differences cause discrete differences in phenotype

Vries significant implication 1

hereditary mechanism produces large changes between generations, so evolution must be saltatory (reject gradualism)

Vries significant implication

continuous variation that biometricians had been reporting must be a consequence of environment

Vries found that

evolution is not gradual, natural selection is not an important mechanism, therefore Darwin must be wrong

development of quantitative genetics

caused by debate of relevance for discrete versus continuous variation in the early 1900s, resolution that individual genes differ

the hardy Weinberg equilibrium led to

the field of population genetics because the consequences of Mendelian Genetics in a population

Until modern synthesis, evolutionary biologists had been interested in

changes in phenotypes over generations, but population genetics portrayed evolution as changes in allele frequencies over generations

genomes

include genic and intergenic regions

genic regions

contain genes - the information to transcribe and translate into proteins

intergenic regions

are not used for protein production

what is in a human genome

only 1.5% protein coding genes, ~27.5% genic regions - introns and exons, lots of transposable elements

mutation is

the ultimate source of all variation

evolution depends upon

the presence of variation and all variation ultimately arises by mutation

the importance of mutation

both the stability and mutability of DNA are fundamentally important to the evolutionary process

the survival of a lineage depends on:

genetic information being passed over generations and remaining intact enough for survival and reproduction, and sufficient variation to allow adaptation to changing conditions

types of mutation

point mutations, insertion, deletion, gene duplication, inversion, chromosome fusion, genome duplication

mutations result form 1)

errors in DNA replication, crossing over, or segregation of chromosomes during meiosis

mutations result from 2)

effects of chemical or physical influences that react with and change structure of DNA

mutations result from 3)

the activity of selfish genetic elements (i.e. transposons)

point mutations

can occur during actual DNA replication causing a change in a single base pair and yields a single nucleotide polymorphism (SNP) in the population if it persists

point mutations - missense mutation

codes for a different amino acid

point mutations - nonsense mutation

codes for a premature stop codon

point mutations - silent (synonymous) mutation

codes for the same amino acid

frame shift mutations

occur when an insertion or deletion is not in a multiple of three bases (shifts whole sequence). Affects translation of other codons in coding DNA

aneuploidy

problems during meiosis can result in extra copies of some chromosomes in some daughter cells

polyploidy

in extreme cases, duplication of the whole genome can occur

chemically of physically induced mutations - UV light

can cause pyrimidine dimer to form when a photon hots a piece of DNA with two adjacent thymidine (TT) or cytosine (CC) base pairs, often detected and repaired but can cause long-term mutations

Chemically or physically induced mutations - many other high energy wavelengths

can also cause a variety of types of DNA damage and mutations

role of environment - air pollution

mutation rate 2X higher near unfiltered industrial sites, paternal but not maternal groups differed due to more opportunities form mutation in sperm

somatic mutations

occur in the cells in the rest of the body (e.g. most forms of cancer causing mutations)

germ-line mutations

occur in the cells that divide to form gametes (the “stuff” of evolution)

cutting edge science

quantifying the fitness effects of mutations and estimating the rate of mutations remains a very challenging task

mutation and the cutting edge of science

the genomic revolution has given us an unprecedented way to study mutations. Scientists are now sequencing many different samples from different types of cancer and finding large differences in mutation profile

population

a group of individuals that have approximately equal probabilities of mating with each other

in order to understand something as complicated as evolution

first we must represent what happens in the absence of evolution, this gives us a null model

genotype

made up of two alleles in diploid individuals

allele frequency

the number of copies of that allele divided by the diploid population size (2N)

genotype frequency

the number of individuals with that combination of alleles divided by the number of individuals (N)

HWE assumption 1)

a single locus with two alleles does not mutate between generations

HWE assumption 2)

no immigration or emigration to/from the population

HWE assumption 3)

the population is very big (infinite), this eliminates the effect of random fluctuations in the frequency of alleles that occur in small populations (no drift)

HWE assumption 4)

there is no natural selection (the fitness of each genotype is equal); survival ability the same, # of offspring the same, equal number of males and females for each genotype

HWE assumption 5)

mating is random with respect to the trait of interest

under random mating

individual gametes have equal probabilities of combining with each other, regardless of the alleles they carry at the locus of interest

because of the HWE assumptions

the frequency of these alleles does not change from one generation to the next

haplotype

haploid genotype of a gamete

under the assumption of random mating: the haplotype of

egg will be independent of the haplotype of sperm as it fertilizes that egg to form a zygote

basic probability theory

the probability of two independent events occurring together is the product of their individual probailities

if we see big deviation from HWE

then we can conclude pronounced evolutionary change might be happening at the locus

the HWE equation can be used

to identify when the basic assumptions are violated

HWE assumes

a population of infinite size undergoing random mating, with no selection, migration, or mutation

a population that is perturbed by a violation of HWE assumptions

will return to HWE in one generation of random mating, once the assumptions are met

we know it’s not in HWE

if we find that the number of both homozygotes genotypes exceeds the number of heterozygotes

if we consider only the complement of alleles that come from one parent or the other

we can study the haplotype frequencies. A haplotype is a way of representing the multi-locus combination of alleles in each gamete

linkage equilibrium

when there is no association between loci above randomness ( observed = expected)

Linkage disequilibrium (LD) or Gametic Phase Disequilibrium

when there is non-random association between alleles at the loci involved

the difference between the observed and expected haplotype frequencies will

differ by the same amount, which is the linkage disequilibrium or D

x1 and x4 are

coupling haplotypes, because they are both upper or lower case

x2 and x3 are

the repulsion haplotypes because they are mixed cases

LD tells use whether

the coupling haplotypes are more (D>0) or less (D<0) associated than expected at random

recombination is

the most important genetic factor affecting association between locus A and B

physical linkage

the distance between loci, occurs on a single chromosome

Model #1 - locus A and B located on two chromosomes

the shuffling of chromosomes: a gamete’s allele at one locus is independent of the allele at the other locus, will produce four types of gametes in equal proportions

model #1 - recombinant genotype

½ gametes are same as parents, ½ differ from parents; probability of recombinant genotype (r ) = 1/2

Model #2 locus A and B are located on the same chromosome

these loci are considered as physically linked, linkage maintains an association between the loci, but this can be broken by recombination

model #2 - during prophase of first meiotic division

homologous chromosomes align with each other, during synapsis one chromatid from one chromosome can cross over a chromatid from the other chromosome, and recombination will occur if this happens between loci r = ½

Model #2 - if crossing over occurs, ½ the chromatids exchange equal pieces

if the probability of crossing over is “c”, then the proportion of recombinant gametes will be: r = c/2

probability of recombination depends on

proximity of two loci on a chromosome and their proximity to the centromere; two loci can be so close together that recombination almost never occurs

x1 = p[a] * p[b] + D; if D > 0

the association between alleles increases the frequency of the x1 haplotype above the random expectation

after one generation of random mating, the frequency of x1’ = p[a] * p[b] + D - rD

so recombination is breaking up the association between these loci (aka: the LD). the opposite happens for D < 0 (i.e. the negative association is broken up)

the amount of disequilibrium decreases by a factor of (r-1) each generation

thus after t generations of random mating, the disequilibrium is: Dt = D (1-r)^t . this applies when loci are on the same or different chromosomes

even with different chromosomes and r = 0.5

LD still decays over several generations

Linkage disequilibrium (LD) is the difference

between observed vs expected frequency of the haplotype. by convention: it is positive when coupling haplotypes are more common than expected

linkage disequilibrium decays

in proportion to how much LD there is already (D) and the rate of recombination (r )