Molecular Evolution

Question 1

Molecular phylogeny

Answer 1

-modern trees are also built using genes, DNA, or speific biomolecules. Transcription products and DNA differ bbetween species and can be used to infer evolutionary relationships
DNA: the entire genome of the species is not compared

Question 2

Chemotaxonomy

Answer 2

Inferring evolutionary relationships based on differences in compounds common across species
ex: proteins, peptides, protoplasm

Question 3

Haplotype

Answer 3

specific region of DNA compared between species

• highly conserved
• likely to be inherited

Question 4

Align sequences

Answer 4

Alignment of the sequences so we can see where teh nucleotides differ

Question 5

Molecular clock

Answer 5

mutation that occur at an average rate over time

• **completely independent of morphological changes, neutral mutations
• Relies on vertical gene transfer only
• how you link a DNA cladogram to real life time
• can infer *when they diverged

Question 6

Calibrate your clock : steps?

Answer 6

1. pick haplotype
2. determine how different this region of DNA is between your groups of interest
3. Calibrate your clock
   To find the time to determine the rate of change the fossil record is usually used (divergence in the two species AKA last common ancestor)

Question 7

2% rule:

Answer 7

on average two lineages tend to diverge from each other in their genome by approximately 2% per million years

Question 8

relaxed molecular clock

Answer 8

def: a molecular clock where the rate of molecular change is allowed to vary between lineages
assumptions:
1. the rate of mutation does vary between organisms and over time, but we can still average this rate to achieve an approximation of the true rate.
2. the rate of mutation itself can change over time and is tied to the rate of change for features under natural selection

Question 9

evolutionary developmental biology (evo devo)

Answer 9

-compares developmental processes across different organisms to infer ancestral relationships

Question 10

deep homology

Answer 10

very dissimilar organs across distantly related groups are controlled by similar genes

Question 11

developmental-genetic toolkit

Answer 11

very few genes control development

Question 12

HOX genes

Answer 12

-bilateral symmetry
-position of the structures in the body plan
(think spinal chord)

Question 13

The molecular wars

Answer 13

• molecular clock argues that DNA mutates at an average rate over time (nothing to do with influences from the environment, a type of genetic drift)
• variation in DNA drives evolution

LED TO M.W.
evolutionary theory was divided between
1. traditional trait-based evolutionary biologists
2. molecular biologists

Question 14

Neutral theory of molecular evolution

Answer 14

At a molecular level: most evolutionary changes are caused by genetic drift of neutral alleles (supported by redundancy in codons)
-At the phenotypic level, evolution is mainly driven by natural selection

Question 15

How do you choose a haplotype?

Answer 15

1. gene common to all species in that study group
2. gene that is guaranteed to be heritable
3. gene that has a slow and steady rate of mutation

Question 16

Limitations of trait based trees?

Answer 16

1. trait based trees do not indicate WHEN species diverged from their last common ancestor (depends on the fossil record for this)
2. do not account for cryptic species
   3 difficulties taking into account convergent evolution (homoplasies)

Question 17

What is the difference between DNA barcoding and molecular phylogeny?

Answer 17

DNA barcoding is used to identify species. Molecular phylogeny is used to compare relatedness and compares using a specific DNA sequence

Question 18

Rate of mutation

Answer 18

many differences: fast rate of evolution
few differences: slow rate
-we only see the mutations that are survivable

Question 19

Limitations of the molecular clock?

Answer 19

-different rates of mutation between species