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Phylogenetics > Phylogenetics Finals > Flashcards

Phylogenetics Finals Flashcards

1
Q

Differences between Gene Trees and Species Trees

A

GT: histories of loci within the genome
ST: reconstructing lineage history

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2
Q

Define Coalescence

A

Point of common ancestry of 2 alleles

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3
Q

Assumptions of allele coalescence

A
  1. Equal probabilities of alleles being passed
  2. Population size is constant overtime
  3. Alleles in generation “t” are drawn randomly with replacement from alleles from the previous generation (t-1)
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4
Q

Probability of coalescence

A

Given N diploid individuals in each generation, the probability that 2 alleles selected randomly in generation coalesce (come from the same parental allele) in the preceding generation t-1 is 1/(2N)

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5
Q

What is the probability that two alleles coalesceded in the previous generation?

A

1/(2n).

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6
Q

Coalescence occurs at a _______rate when the population is large. Why?

A

Slower. With more individuals within a population, there is a decrease in the likelihood that you’ll find an allele that matches up with your LCA and the related species’ population.

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7
Q

The expected time to coalescence of 2 alleles

A

2n.

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8
Q

Why moving from tip to stem, does it take longer than 2N for allele coalescence time?

A

As populations increase in size, allele frequencies within each individual become more disparate. Therefore, the larger the population, the slower the CT.

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9
Q

What causes coalescent histories of different genes sampled from the same individuals to have different topologies?

A

Recombination.
Each gene might show a slight deviation from the next due to their lack of identical code.

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10
Q

Genes of different chromosomes are likely to have ________ histories.

A

Disocordant

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11
Q

What are recombinational genes?

A

a block of adjacent nucleotides sharing the same gene tree. This is the ideal locus for phylogenetic inference. In practice,
functional genes are assumed to be recombinational genes

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12
Q

Why does deep coalescence kind of ruin species trees?

A

Because a shared allele (coalescence) typically occurs before an LCA of two species. The allele surfaces first and then carries into the two sister species.

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13
Q

Coalescences are more likely in: (narrow and long) or (short and wide) trees? Why?

A

Narrow and long. Narrow denotes smaller populations, therefore there is an increased likelihood of shared alleles

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14
Q

Anomaly Zone. What is it?

A

If both internal branches are sufficiently short, then coalescence is not likely until back near the base node. This means that the population tree does not reflect the gene tree

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15
Q

Approaches to avoid gene tree discordance (there are 4)

A
  1. Majority rule consensus
  2. Concatenate all sequences (assumes all genes have same history)
  3. Use multi-species coalescent
    (assumes discordance is due to deep coalescence)
  4. Bayesian concordance analysis
    (assumes genome proportions for which individual clades are true)
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16
Q

Concatentation

A

laying gene elements end-to-end, creating a supermatrix

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17
Q

How to minimize DC using parsimony

A
  1. Count the min # of dp events in a tree
  2. search among candidate. tree to minimize
    Drawback: only topology is estimated
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18
Q

What is a population tree

A

Branch lengths (time in generations), and branch widths (ancestral population size)

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19
Q

Sequence data in gene trees with branch lengths are measured in ________

A

mutations per site

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20
Q

Causes of gene tree discordance (3)

A
  1. deep coalescence
  2. paralogy. (gene duplication and loss)
  3. horizontal gene transfer
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21
Q

What does “trees within trees” mean

A

Gene trees within population trees

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22
Q

define Orthologs

A

SAME. genes in different species that share the same locus and function

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23
Q

define Paralogs

A

DIFFERENT. genes related by duplication. positioned at DIFFERENT loci, different functions

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24
Q

Explain horizontal gene transfer

A

Transfer effected WITHOUT mating.

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25
Q

What can cause congruences between hosts and parasites (3)

A
  1. Duplication (speciation)
  2. Host switching or range expansion
  3. unequal heterogenous rates of molecular evolution
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26
Q

How to assess congruence? (5)

A
  1. compare tree topologies
  2. Use independent calibrations of host and parasite molecular clocks
  3. Measure homogeneity of data
  4. Does the analysis fail to pick 1 tree?
  5. Reconciliation analysis (host tree fits with parasite tree)
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27
Q

Define (generally) “Species”

A

Basic unit of biological diversity

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28
Q

Ernst Mayer emphasized _____ when defining species

A

Interbreeding populations isolated from other communities

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29
Q

Biological Species concept

A

populations of organisms connected by gene flow and separated from other species by reproductive barriers

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30
Q

Genotypic concept

A

Species based on identifying phenotypic or genotypic clusters of individuals (i.e., things more similar to each other, and less to others).
Issues: morphs? sex differences?

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31
Q

Mallet: pattern vs process

A

Pattern: retain differences in sympatry
Process. Reproduction, hybrids, natural selection

32
Q

Phylogenetic species concept:

A

shared derived characters define species

33
Q

Three species concepts

A

Biological, Genotypic, phylogenetic

34
Q

Baum harps on groups as being _______

A

exclusive. Things that form a clade from more of the genome than any other conflicting set.

35
Q

Baum. Taxa vs functional units

A

Taxa: products of history or evolution
Function: trait-based, biological species concept

36
Q

Define Discordance

A

variance in the histories tracked by different genes for a set of individuals

37
Q

Recognizing HGT

A

gene trees where an organism shows a gene that is not associated with its related group

38
Q

Mark of hybridization (genetically)

A

A mix of genetic blocks (about 50/50 distribution)

39
Q

Introgression

A

Back crossing from hybrids. The bits of foreign genes from the hybrid get introduced into one of the initial genomes

40
Q

Primary concordance tree

A

composed of clades that. have higher concordance factors than any alternative clade

41
Q

Concordance factors are estimated for:
(there are two)

A
  1. A sample of genes
  2. genome as a whole
42
Q

How to determine by looking at a figure if it’s ILS or Gene Flow?

A

if ILS, then primary concordance tree gives the true results, and the remaining values are split between two possibilities. (80% true, then 10%, 10%)

43
Q

What pattern do we expect with hybridization speciations?

A

2 co-primary trees

44
Q

D-Statistics. What are they and why do we use them?

A

If you have a topology with three in group, and one outgroup, then you can get different possibilities.

45
Q

D STAT statistic example

A

C(ABBA)-C(BABA) / C(ABBA)+C(BABA)

46
Q

D stat does not allow testing for what?

A

Testing between sister groups

47
Q

D stats approaching 0 mean ______ and approaching 1 means________

A

0 - ILS
1 - Introgression

48
Q

Two classes of characters

A

Discrete: categorical
Continuous: measurements

49
Q

Chronicle vs Narrative

A

Chron: how
Narrative: why

50
Q

Steps in testing hypo of adaptations on a phylogeny (6)

A
  1. infer a tree
  2. score traits
  3. score selective regimes
  4. reconstruct history of character changes
  5. reconstruct history of selective regimes
  6. assess current utility
51
Q

Define selective regime

A

Abiotic and biotic factors that determine how natural selection will act on a character

52
Q

Dollo’s Law

A

concept of irreversibility

53
Q

Describe ancestral state reconstruction

A

Tracing back characters (features) through the tree to predict the ancestor’s state of that given trait

54
Q

Phylogenetic covariance

A

If traits evolve completely at random, then the expected effect is the phylo tree. Time which two taxa have been evolving together

55
Q

If phylo covariance is high, then_____

A

the species will be very similar

56
Q

In Brownian motion, where would you expect two branches to eventually end up?

A

Where they split. Closer=higher variance

57
Q

Define contrasts

A

Difference between two tip states. First between sisters. Expected value of 0

58
Q

Normalized contrast

A

Divided by the two lengths of the branches they are on. EXAMPLE (A-B)/(v1+v2)

59
Q

Weighted Averaging

A

X1 = (Av2 + Bv1)/(v1+v2)

60
Q

Know what inherent statistical issues there are with contrasts, and how normalized contrasts solves it

A

Normalizing helps reduce the greater covariance between species with deeper ancestral nodes

61
Q

GLS allows for _____ and ______ unlike ordinary least squares

A
  1. Unequal variances
  2. Nonindependance
62
Q

Brown motioning assumes.
1. Close individuals have ___trait values
2. high variance between _______related taxa

A
  1. similar
  2. distantly
63
Q

Know how to test a rate shift hypothesis

A
64
Q

What do indépendant contrasts accomplish? (3)

A
  1. reduces autocorrelated results
  2. Normalization reduces distances between taxa
  3. Reconstruct the ancestral state
65
Q

What evidence could there be that the dentist passed HIV to his patients? (forensic epidemiology)

A

All strains contained within a single clade

66
Q

Processes that influence the shape of virus phylogenies: (3)

A

1.directional selection
2. spatial structure
3. changes in population size

67
Q

What does a balanced tree indicate?

A

A lack of directional selection (weak selection)

68
Q

What do the following entail in the context of viral population trees?

  1. Long trunk, short tips
  2. Short trunk, long tips
A
  1. constant pop size
  2. Exponentially increasing pop size
69
Q

Species diversity

A

measures how many species in a given area

70
Q

Functional diversity

A

ecological variation present among the species in an area (using traits as a proxy for function)

71
Q

Phylogenetic diversity

A

how much phylogenetic history is represented by the species present

72
Q

Phylogenetic Cluster vs Overdispersion

A

Cluster: traits are confined to clades
Over: traits observed are scattered across the tree

73
Q

Phylo clustering is treated as evidence for…

A

ecological filtering

74
Q

phylo over dispersion is treated as evidence for…..

A

competitive exclusion. (closely related species are not in the same habitats since they would battle against each other)

75
Q

How we can calculate phylogenetic diversity

A

total length of the minimum spanning path connecting a subset of species on a tree (so total branches present). Only in the species present

76
Q

What is evolutionary distinctiveness?

A

ED used for single species or a branch. For a single branch: length of the branch divided by the number of descendants.
For single species: sum of branch scores along the path to the root

77
Q

EDGE. what is it?

A

ED + GE (Global extinction risk)

Phylogenetics (2 decks)

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