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Evolution > Exam 3 > Flashcards

Exam 3 Flashcards

1
Q

What are Mendelian traits?

A

discrete traits produced by a single locus or 2/3 loci

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2
Q

What are quantitative traits?

A

continuous traits produced by a large number of genes

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3
Q

What do selection gradients measure?

A

only the phenotypes relative to fitness

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4
Q

How can discrete entities (genes) produce traits with continuously varying values?

A

Because number of combos of genes are bigger and the differences between the traits are small

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5
Q

Complete additivity

A

Adding the affects of each allele

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6
Q

Directional selection

A

favors one side of extreme (linear graph)

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7
Q

Stabilizing selection

A

favors the mean value (distribution graph)

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8
Q

Disruptive selection

A

favors both extremes (parabola)

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9
Q

Quantitative trait loci (QTLs)

A

regions of the genome containing genes that influence quantitative traits

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10
Q

Genetic mapping

A

based on recombination rates

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11
Q

Physical mapping

A

based on sequencing (finds exact distance)

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12
Q

What is a single nucleotide polymorphism SNP?

A

something we can identify in the chromosome that lets us figure out the position in the chromosome (genetic marker)

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13
Q

How does QTL mapping work?

A
  • Find two parents that differ in the trait of interest (easier if inbred)
  • Make genetic maps of each parent ( with unique and shared markers to tell where a particular gene comes from)
  • cross parents to get F1 offspring
  • Self/inbreed F1s to get recombinant inbred lines (RILs)
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14
Q

Why are RILs important?

A

we end up with individuals who are homozygous at every locus but will be made up of different combinations of the parental genomes

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15
Q

What does QTL mapping tell us from an evolutionary context?

A

It can show us what part of the chromosome is important to make that specific change

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16
Q

What are some characteristics of GWAS (genome-wide association studies)

A

-QTL on a massive scale
-uses many thousands of SNPs
- with many thousands of individuals (not just two parents)
-genotypes every single individual
-Have to correct for multiple comparisons
-p-value= probability of seeing this association just by chance (below threshold are significant)
- generates Manhattan plot

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17
Q

GWAS vs QTL

A

GWAS:
-natural variation (more genetic variation)
- not only dealing with two parents (allows us to find more of the genetic variation that is affecting that species)
-many markers for fine scale mapping
-expensive
-only suitable for model organisms
QTL:
-only variation between parents is assessable
-usually uses fewer markers
- can use with more organisms
- less expensive

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18
Q

Candidate loci/genes

A

With some prior knowledge you can attempt to predict that certain genes/loci are going to be important genes.
-Not very reliable

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19
Q

Some possible follow up studies:

A

-targeted mutagenesis : to figure out which mutations affect function
-cell culture: can be used to apply evolutionary relevant treatments
-expression: expression level may be a more important evolutionary mechanism than protein changes
-Knockout: to assess effect of gene
-gene phylogeny: to assess evolutionary origin

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20
Q

What is the simplest molecular evolution?

A

a point mutation

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21
Q

Point mutation

A

change of a single nucleotide from one base to another

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22
Q

Types of point mutations

A

Transitions -> purine to purine (A, G) or pyrimidine to pyrimidine (C, T)
Transversions -> Purine to pyrimidine and vice versa

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23
Q

Jukes-Cantor Model

A

a model where everything changes at the same rate
- for every one transition there are two transversion changes ( in categories of changes)

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24
Q

Characteristics for rate of substitution

A
  • It is higher for transitions than transversions
  • it is slower than the mutation rate
  • it is usually higher for synonymous positions in a coding region than for nonsynonymous positions
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25
Q

Substitution

A

If a mutation replaces the original base pair in the population, it is a substitution

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26
Q

How to measure the rate

A

Example:
You have sequences from 2 species. Each sequence is 50 bp long, and they differ at 7 positions. In addition, the species’ most recent common ancestor is estimated to have lived 2.5 million years ago. What is the rate of substitution per site per million years (sub/site/million years) for those sequences in those species?

7/50 = 0.14
sub rate= 0.14 sub/site / 5 million yr = 0.028 sub/site/million

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27
Q

General time reversible model (GTR)

A

get a good estimate of what the relationships are

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28
Q

Fossil rate of evolution

A

how rapidly a character in a species or lineage evolved over time (mostly characteristics of hard body parts, bone, teeth, shells.)

29
Q

Rate of change equation

A

r = (ln(x2) - ln(x1))/ delta t

30
Q

Unit darwin (d)

A

change of power of e per million years
1+e^1 = 1 d

31
Q

Bradytelic

A

slow evolution

32
Q

Horotelic

A

typical rate of evolution

33
Q

Tachytelic

A

rapid evolution

34
Q

MacFadden’s Study

A

Examined four characteristics from many horse’s teeth and calculated the rate of change for 26 ancestor descendant pairs of species for each character. The results showed that the rates of evolution in horses’ teeth indicate the characters studied are not produced by the same developmental genes. For some ancestor-descendant pairs the rates of change for the characters were not identical, some either got larger or smaller. If under common genetic control the same gene would be responsible for development and we would expect them to change in the same direction (pos or neg) and by the same amount.

35
Q

Why do rates of evolution vary?

A
  • rates might be more rapid during period of speciation
    -more genetically complex forms (more genes that determine a trait) can evolve more extreme forms than less complex ( so more genes for variation that selection can act on)
    -some groups evolve more rapidly than others
    -Artifact of the data (there may be systematic differences due to how long you look at a fossil record)
36
Q

Mechanism of artifact

A

evolution varies over time and even changes direction, so shorter intervals are more likely to capture short term rapid changes and give the appearance of greater amounts of change.
selection isn’t constant

37
Q

C-value paradox

A

C-value: measure of diploid genome size in picograms (pg)
The amount of DNA in a diploid genome does not seem to correspond with the complexity of the organism.

38
Q

Why do some protists have larger genomes than a human or onion?

A

The DNA content and the proportion that codes for proteins play a role in explaining the c paradox. A 100% linear correspondence means there is a 1:1 ratio between size of the genome and total amount of that genome that is for the coding of genes. So protists have a 100% correspondence while animals have 1% correspondence

39
Q

Transposons ( Mobile genetic elements)

A

pieces of DNA that can copy themselves and insert themselves to other DNA

40
Q

Mobile genetic elements

A
  • described as genomic “parasites”
  • insert themselves into genomes and replicate (potentially at the expense of the cell)
  • uses transcriptional machinery of the cell
  • like a retrovirus, but never leaves the cell
41
Q

The fact that we find some vertebrate species have over 90% of their genome consisting of MGEs and other vertebrate species have less than 1% of their genomes consisting of MGEs supports what?

A

it supports the fact that there is no clear evidence that transposons are performing some critically important function and that is why we have so many of them in our genomes.

42
Q

Why are eukaryotic genomes junky and not prokaryotic?

A

eukaryotes tend to have smaller populations than prokaryotes, maybe even small enough that drift dominates (escapes selection so transposon cant be removed)

43
Q

Evolved defenses against MGEs

A
  • Methylation: highly methylated so they cannot be transcribed and replicated
  • RNAi: target stretches of MGEs, rendering them immobile after transcription
44
Q

How did Linnaeus identify species?

A

Species were determined by their appearance (Phenetic species concept)

45
Q

Type specimen

A

One specimen that is picked that “best represents” that species

46
Q

Cluster statistics

A

a method to measure as many traits as possible on multiple organisms by grouping things together from by a combo of their similarities

47
Q

Horizontal species concept (ahistorical)

A

concept that defines species at a moment in time

48
Q

Vertical species concept (historical)

A

concept that defines species from the time of their inception until they speciate or go extinct

49
Q

Biological Species Concept (BSC)

A

An interbreeding group with isolating mechanisms that prevent them from breeding more widely (keeps them grouped together)
-cant mate with someone too different bc then offspring will not survive (why species look similar)

50
Q

Reproductive isolating mechanisms

A

-Prezygotic: things that stop things from interbreeding before a zygote gets formed
-Postzygotic: things that happen after zygote is formed that makes a diploid that stops successful interbreeding.

51
Q

Prezygotic mechanisms

A
  1. Geographical isolation: never have the opportunity to breed bc they are too far away
  2. Ecological isolation: Occupy different habitats (where they prefer to be)
  3. Temporal isolation (seasonal or diurnal): timing of things don’t work
  4. Behavioral isolation: have different behaviors so don’t choose to mate with each other
    5.Mechanical isolation: the parts don’t fit right (literally)
  5. Gametic isolation: sperm has to be able to recognize the egg to fertilize it
52
Q

Postzygotic mechanisms

A

-F1 hybrid inviability (dies due to developmental problems)
-F1 hybrid sterility (can’t reproduce so dead end genetically)
-Hybrid breakdown (genetic failure in the F2 generation)

53
Q

Recognition Species Concept (RSC)

A

a group of organisms that have a “shared mate recognition system” (SMRS) which they use to identify appropriate mates. Eliminates individuals and provides cohesion bc will only mate with limited individuals.

54
Q

Cladistic species concept

A

a lineage of interbreeding organisms that begins when its parental lineage is divided into two species and ends when extinct or it speciates

55
Q

Allopatric speciation

A

When you have one big population and then they geographically separate, and later will both genetically differ bc they live in different areas, and sometimes come back together again.

members of a population are separated by a geographical barrier
-Large scale: oceans, mountains, plate tectonics (vicariance events)
-Small scale: peripheral isolates

56
Q

Parapatry

A

The population gets separated but they maintain a contact zone, while still being genetically different, where interbreeding could take place and they become two new species

57
Q

Sympatry

A

population does not separate and live in the same area but can still create two new species

58
Q

What forces would be expected to genetically differentiate two populations through allopatric speciation?

A

Environments may change so selection will act on them differently

59
Q

Incompatibility from a single locus?

A

A single locus is not expected to have a huge affect that will kill off the hybrid since it has survived in the population before

60
Q

Dobzhansky-Muller incompatibilities (2 loci interacting)

A

Theoretically, a new interaction between two loci that hasn’t happened before in the population is introduced that could kill hybrids

61
Q

Allopatric Speciation: Peripheral Isolates

A

Population expands while conditions are favorable and when conditions are unfavorable, it contracts. BUT peripheral isolates are created if the population finds places where it can survive even when conditions got bad, and so those population start to evolve independently and can change enough to where they’ll speciate

62
Q

Developmental biases

A

when natural selection has acted in the past on certain traits, so in an experiment it helps produce prezygotic isolation mechanisms.

63
Q

A Natural Experiment

A

To check to see if patterns that happen in nature match our expectations

64
Q

Clines

A

Changes that we see along some geographic range and may vary sexual compatibility among the species

65
Q

Secondary contact

A

when populations come back to each other after being allopatric (geographically separated)

66
Q

Three possible outcomes after secondary contact

A
  1. Speciation is complete
  2. The process of speciation started but not different enough to where they can’t interbreed with one another freely, so become a common gene pool
  3. The incipient species undergo reinforcement
67
Q

Reinforcement

A

When the process of speciation has started (they’ve begun to differentiate from each other) and there’s some diminishment of their fitness as hybrids but not enough to stop them from interbreeding completely. So selection can act on individuals who prefer to mate assortatively (not with hybrids) and that could complete the speciation process.

68
Q

Does reinforcement work in allopatric speciation?

A

genetically doesn’t work in most cases (only if hybrids are really unfit)

Evolution (2 decks)

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