Week 4: Phylogeography Flashcards

1
Q

What is phylogeography?

A

the study of processes that influence the distribution of phylogenetic lineages

  • relationship between species, space, and time
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2
Q

What are 3 historical evolutionary processes we might be interested in?

A
  • dispersal
  • founder effect
  • vicariance
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3
Q

How did glaciation affect salmon phylogeography?

A
  • ice melting made more rivers accessible, salmon slowly moved in (high site fidelity)
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4
Q

What is a pro/con to unipaternally inherited markers in phylogeography?

A
  • simple lineage tracking
  • single locus, sensitive to bottlenecks
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5
Q

What is a pro and con of using microsatellites in looking at evolutionary history?

A
  • highly variable (lots of alleles)
  • size homoplasy
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6
Q

What is a benefit of SNPs in looking at evolutionary history?

A
  • many de novo markers - high resolution genome-wide

(technical challenges/cost are no longer limiting)

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7
Q

What does having more loci do for a phylogeography study?

A

shows finer scale evolutionary relationships

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8
Q

How many loci do we need for phylogeographic studies?

A
  • depends on study context
  • diminishing returns past 5000 loci
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9
Q

In phylogenetics, how do we use parsimony?

A
  • The most likely phylogeny has the fewest individual mutations
  • mutations that occur less often happened more recently
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10
Q

What is a molecular clock?

A

using sequence divergence to estimate evolutionary time, assuming mutation rates are constant

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11
Q

What are three reasons there is no universal molecular clock?

A
  • different mechanisms of mutation have different rates
  • different regions of the genome have different rates
  • different species have different mutation rates (life history and generation time)
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12
Q

What is one application of molecular clocks?

A
  • CALIBRATE WITH FOSSIL DATA
  • checking if Darwin’s moth and that flower co-evolved – shows that co-evolution might predict species emergence
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13
Q

Name the three types of phylogenetic trees we need to know.

A
  • rooted, scaled tree
  • rooted, unscaled tree
  • unrooted tree
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14
Q

Which phylogenetic tree displays the timing of divergence?

A

the scaled rooted tree

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15
Q

What is a distance-based tree?

A
  • tree based on genetic ‘distance’ between taxa
  • simplified method using individual sequences
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16
Q

What is a maximum parsimony tree?

A
  • tree with minimum number of evolutionary changes
  • assumes constant mutation rate between taxa, works best on closely related taxa
17
Q

What is a maximum likelihood tree?

A
  • tree that uses a specific evolutionary model to make observed data most probable (complex statistics)
18
Q

What is a Bayesian phylogenetic tree?

A

trees made from Bayesian statistical models

19
Q

For maximum likelihood phylogenetic trees, how are probabilities generated?

A

BOOTSTRAPPING

20
Q

What do nodes measure in Bayesian phylogenetic models?

A

the posterior probabilities the tree is correct

21
Q

What do phylogenetic trees measure?

A

lineage sorting

22
Q

What variation do phylogenetic trees miss?

A
  • fine-scale recent variation (gene specific)
  • co-existence of ancestors and descendants
  • rejoining of lineages
23
Q

What is the coalescent?

A
  • how alleles originated from a most recent common ancestor
  • mathematical model generates backward lineages to see where alleles ‘coalesce’
  • generates HAPLOTYPE NETWORKS
24
Q

What is a haplotype network?

A

visible representations of networks of haplotypes
- size = frequency of haplotype
- length = number of mutations

25
Q

What does it mean if a haplotype has more connections (in a haplotype network)?

A

It is probably older

26
Q

What species have haplotype networks been used to

A

an Argiope spider,
- argued new species under the genetic species concept

27
Q

how did glaciation affect phylogeography?

A

pushed species into climate refugia (ex trembling aspen)

28
Q

What are climate refugia?

A
  • hospitable areas in an inhospitable matrix
29
Q

What are two main models of small scale phylogeography?

A
  • dispersal
  • vicariance
30
Q

What is the vicariance model?

A

parts of a population get separated by the environment changing, leading to isolation/speciation
(ie. a continuous population is cut off by barriers to dispersal)

31
Q

What is the dispersal model of species distribution?

A
  • species movement, dispersal and colonization influence speciation/distribution
32
Q

What is an example of vicariance and dispersal changing species distributions?

A

The ishtmus of Panama closing off - cause marine populations to be cut off, creates pathways for terrestrial species to disperse