Phylogenetics

Question 0

Phylogenetic tree

Answer 0

Graphical summary of inferred phylogeny, marks on limbs mark new traits

Question 1

Phylogenetics

Answer 1

The study of evolutionary relationships among taxa

Question 2

Sister taxa

Answer 2

Closest relatives

Question 3

How to determine similarities/differences in phylogenetic trees

Answer 3

Look at sister taxa, swing branches around in head if necessary

Question 4

Characters for phylogenetic analysis

Answer 4

Morphology (historically), behavior, physiology, biochemistry, DNA or protein sequences (today)

Question 5

Characters for phylogenetic analysis require

Answer 5

Being independent of each other (characters not closely related), variable among taxa due to genetic differences (not environmental), reflect homology

Question 6

Homology

Answer 6

Similarity due to common ancestry, useful in phylogenetic analysis

Question 7

Analogy

Answer 7

Similarity not due to common ancestry, confuses phylogenetic analysis

Question 8

Convergence

Answer 8

Type of analogy, independent evolution of a similar trait (ability to fly in birds and bats)

Question 9

Reversal

Answer 9

Type of analogy, loss of diverged trait or loss of new trait (loss if wings in flightless birds)

Question 10

Synapomorphy

Answer 10

Shared, derived character state, reflect homology, useful in phylogenetic analysis (trait along the main branch that distinguishes one set of species from another - tetrapods, amniotes, reptilia)

Question 11

Symplesiomorphy

Answer 11

Shared, primitive character state, old homology or trait shared beyond the group, not useful (something further back when referring to just one group - amniotic egg for crocs and birds since reptilia still in that classification too)

Question 12

Autapomorphy

Answer 12

Unique, derived character state, not shared by multiple groups, not useful (trait that is present just in that one species - feathers for birds)

Question 13

Cladistics

Answer 13

A way to infer relationships among taxa using principle of parsimony

Question 14

Parsimony

Answer 14

Simpler hypotheses are preferred over more complex hypotheses

Question 15

Parsimony informative

Answer 15

Must have at least two states, each represented at least two times - TTTCC is because T and C are both present twice at least

Question 16

Parsimony uninformative

Answer 16

Not having at least two states two times each at least - GGGGG is not because it only has one state, AAGCT is not since there are not two each

Question 17

Preferred phylogeny identification

Answer 17

Compare all possible trees, sum the # of character states across all characters for each tree, the preferred tree is the one that implies the lowest overall character state changes

Question 18

Bootstrapping

Answer 18

Randomly sampling characters from the data set to estimate support for each branch of the tree (%age means how sure this branch goes there and >70% is a good thing)

Question 19

Monophyletic group

Answer 19

Includes all descendants of common ancestor

Question 20

Paraphyletic group

Answer 20

Includes only some descendants of a common ancestor

Question 21

Polyphyletic group

Answer 21

Usually a mistake, includes distantly related species not sharing a recent common ancestor

Question 22

Taxonomic classification should include

Answer 22

Monophyletic groups because they are more based on genetics and show similar relations in genes not just appearance

Question 23

Coevolution

Answer 23

Evolving together with changes in the environment and mutations

Question 24

Cospeciation

Answer 24

Separate species evolve along similar lineages due to their relationships (aphids and bacteria)

Question 25

Phylogenetic trees to detect cospeciation

Answer 25

Look and see if divergence of two species looks similar in terms of time and how it branched (% support)

Question 26

Phylogenetic trees to study adaptation

Answer 26

Comparative method, look at the order of changes based on tree, if this adaptation evolved before another then the second one isn’t an adaptation but rather a pre-adaptation

Question 27

Phylogenetics and disease transmission

Answer 27

Look at which species has which virus species when based on genetic information and look and number of changes