Module 3

Question 1

DNA barcoding

Answer 1

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

Question 2

Barcoding gap

Answer 2

Gap in variation within a species to between species

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

Question 3

Biological species concept

Answer 3

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

Question 4

Tips

Answer 4

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

Question 5

Nodes

Answer 5

Most recent common ancestor, can rotate

Question 6

Monophyletic clade

Answer 6

Natural grouping of node and all tips and ancestors

Question 7

Paraphyletic clade

Answer 7

Non natural groupings of selected tips and/or ancestors

Question 8

Branches

Answer 8

Edges or internodes

Question 9

Phylogram

Answer 9

Tree that models rate of change

Question 10

Chronogram

Answer 10

Tree that indicates absolute time

Question 11

Roots

Answer 11

Starting points

Informs outgroup of rooted trees

Question 12

Synapomorphy

Answer 12

Characteristic shared bw ancestor and all evolutionary descendants

Question 13

Analogies

Answer 13

Traits shared by unrelated species through convergent evolution

Question 14

Autapomorphy

Answer 14

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

Question 15

Distance based phylogeny

Answer 15

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

Question 16

UPGMA

Answer 16

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

Question 17

NJ (neighbor joining)

Answer 17

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

Reduces overall length if tree -> shortest tree

Question 18

ME (minimum evolution)

Answer 18

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

Question 19

Observed distance

Answer 19

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

Question 20

Genetic distance

Answer 20

The total amount of mutations that occur between two taxa

Question 21

Discrete character

Answer 21

Tree searching method that finds best evolutionary explanation for taxonomy

Question 22

Maximum parsimony

Answer 22

Discrete character method

Functions on concept that the fewest change possible is best

Mist common for non-molecular data

Question 23

Maximum likelihood

Answer 23

Discrete character method

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

Question 24

Bootstrap

Answer 24

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

Question 25

Rearrangement methods of ml

Answer 25

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

Question 26

Hill climbing approach

Answer 26

Optimizes trees by only using best tree to proceed Has issues with local optimization

Question 27

Bayesian phylogenetically

Answer 27

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

Question 28

Markov chain Monte Carlo (mcmc)

Answer 28

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

Question 29

Mc3

Answer 29

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

Question 30

Maximum a posteriori (MAP) tree

Answer 30

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

Question 31

Majority rule consensus tree

Answer 31

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

Question 32

95% credible set

Answer 32

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

Question 33

Molecular clock hypothesis

Answer 33

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

Question 34

Rate heterogeneity

Answer 34

Rates of evolution differ among lineages

Question 35

Strict clock model

Answer 35

All branches have same rate of change

Question 36

Local clock model

Answer 36

Clusters rates and branches

Question 37

Relaxed branch

Answer 37

Rate for each branch, impossible to directly estimate

Question 38

Phylogeny calibration

Answer 38

Uses known events to date tree Like fossil data

Question 39

Phylogenetic comparative methods (PCM)

Answer 39

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

Question 40

Phylogenetic non independence

Answer 40

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

Question 41

Species richness

Answer 41

The number of different species in a given area = speciation - extinction

Question 42

Speciation

Answer 42

Splitting of ancestral lineage into 2 evolutionarily independent descendant lines

Question 43

Extinction

Answer 43

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

Question 44

Phylogenetic imbalance

Answer 44

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

Question 45

Phylogenetic diversification timing

Answer 45

Refers to when clades split Early may be due to adaptive radiation while late may be due to island pops

Question 46

Lineage through time (LTT) plots

Answer 46

Counts each time it branches off until tips are reached to investigate diversification rates 3 different models: constant, abrupt, and gradual

Question 47

Gamma stat

Answer 47

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