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Bz5450:module 2/3 > Module 3 > Flashcards

Module 3 Flashcards

1
Q

DNA barcoding

A

Identifying samples to species based on a short, standardized gene sequence

Uses co1 for animals and rcbl and mark for plants

Issues include that it doesn’t distinguish ancestral polymorphisms, male based gene flow, selection on mtdna, gene flow after hybridizations, transfer bw mtdna and nuclear, recent speciation, slowed rates of molecular evolution

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2
Q

Barcoding gap

A

Gap in variation within a species to between species

Assumes separate species will have a greater degree of variation than within species

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3
Q

Biological species concept

A

A species is group of interbreeding populations with unique genetic identities and are reproductively isolated from other populations allowing for independent evolution

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4
Q

Tips

A

End of the process, usually present day. Taxonomic level depends on research question

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5
Q

Nodes

A

Most recent common ancestor, can rotate

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6
Q

Monophyletic clade

A

Natural grouping of node and all tips and ancestors

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7
Q

Paraphyletic clade

A

Non natural groupings of selected tips and/or ancestors

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8
Q

Branches

A

Edges or internodes

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9
Q

Phylogram

A

Tree that models rate of change

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10
Q

Chronogram

A

Tree that indicates absolute time

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11
Q

Roots

A

Starting points

Informs outgroup of rooted trees

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12
Q

Synapomorphy

A

Characteristic shared bw ancestor and all evolutionary descendants

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13
Q

Analogies

A

Traits shared by unrelated species through convergent evolution

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14
Q

Autapomorphy

A

A distinctive feature/derived trait that is unique to a given taxon

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15
Q

Distance based phylogeny

A

Uses measures of overall similarity to compare taxa by creating distance (not genetic) matrices b/w samples

Quick, easy, initial approximation but not v accurate

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16
Q

UPGMA

A

Unweighted pair group methods with arithmetic means used as a distance based method to cluster OTUs

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17
Q

NJ (neighbor joining)

A

Clustering method of distance based trees that pairs neighbors connected by a single node.

Reduces overall length if tree -> shortest tree

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18
Q

ME (minimum evolution)

A

Distance based optimization method that produces the shortest branch lengths (minimum distance)

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19
Q

Observed distance

A

Genetic distance considered by distance methods (only measures difference bw input and output)

20
Q

Genetic distance

A

The total amount of mutations that occur between two taxa

21
Q

Discrete character

A

Tree searching method that finds best evolutionary explanation for taxonomy

22
Q

Maximum parsimony

A

Discrete character method

Functions on concept that the fewest change possible is best

Mist common for non-molecular data

23
Q

Maximum likelihood

A

Discrete character method

Tests the probability of the hypothesis of the data to match a given tree

24
Q

Bootstrap

A

Resampling/ testing of the data to provide support for ML method

25
Q

Rearrangement methods of ml

A

Nearest neighbor joining (NNI)
Sub tree pruning and regrafting (SPR)
Tree bisection and recombination (TBR)

26
Q

Hill climbing approach

A

Optimizes trees by only using best tree to proceed

Has issues with local optimization

27
Q

Bayesian phylogenetically

A

Finding the best option in tree space by using prior knowledge to inform tree searching

28
Q

Markov chain Monte Carlo (mcmc)

A

Random walking through tree face that allows all uphill transitions, slight downhills but negates drastic downhills

29
Q

Mc3

A

Uses cold chains and hot chain robots (scouts) to optimize mcmc approach

30
Q

Maximum a posteriori (MAP) tree

A

After Bayesian methods
Topology with max posterior probability (like ml tree)

31
Q

Majority rule consensus tree

A

After Bayesian methods

Constructed w/o that it contains all clades that occur in at least x% of trees in distribution

32
Q

95% credible set

A

After Bayesian methods

The set of all tree topologies that account for 95% of posterior probability

33
Q

Molecular clock hypothesis

A

Mutation rate has a rate of change and sequence divergence is proportional to time

34
Q

Rate heterogeneity

A

Rates of evolution differ among lineages

35
Q

Strict clock model

A

All branches have same rate of change

36
Q

Local clock model

A

Clusters rates and branches

37
Q

Relaxed branch

A

Rate for each branch, impossible to directly estimate

38
Q

Phylogeny calibration

A

Uses known events to date tree

Like fossil data

39
Q

Phylogenetic comparative methods (PCM)

A

Analytical study of species, populations, and individuals in a historical framework to elucidate the mechanisms at the origin of the diversity of life

40
Q

Phylogenetic non independence

A

Related species may share the same traits which violates the assumption of independence for biological data

A single heritable change can be inherited by many descendants and get counted multiple times

41
Q

Species richness

A

The number of different species in a given area

= speciation - extinction

42
Q

Speciation

A

Splitting of ancestral lineage into 2 evolutionarily independent descendant lines

43
Q

Extinction

A

Termination of a branch in a phylogenetic tree. A branch with no living descendants

44
Q

Phylogenetic imbalance

A

How taxa are distributed among different clades of a phylogeny

Low may be due to competition while high may be due to heritable characters that effect diversification

45
Q

Phylogenetic diversification timing

A

Refers to when clades split

Early may be due to adaptive radiation while late may be due to island pops

46
Q

Lineage through time (LTT) plots

A

Counts each time it branches off until tips are reached to investigate diversification rates

3 different models: constant, abrupt, and gradual

47
Q

Gamma stat

A

Used to measure if per-lineage speciation and extinction rates have remained constant through time

Bz5450:module 2/3 (2 decks)

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