Quest 2

Question 1

What are the two hypotheses you can ask with phylogenetics?

Answer 1

1) relationships and pattern of evolutionary processes.
2) phylogenetics allow us to test past hypotheses.

Question 2

Phylogenetic Systematics

Answer 2

Organizing life based on evolutionary history

Question 3

Phylogeny

Answer 3

Branching relationships of populations as they give rise to multiple descendents populations over evolutionary time.

Question 4

Phylogram

Answer 4

Phylograms have branch lengths proportional to the amount of evolutionary change (e.g., genetic mutation rate).

Question 5

Cladogram

Answer 5

show only the branching pattern (topology) of relationships, with all branch tips aligned and no specific meaning to branch lengths

Question 6

Chronogram

Answer 6

Showing actual time at divergence (usually used in paleontology)

Question 7

Node

Answer 7

Common ancestor

Question 8

Branch

Answer 8

Descendents

Question 9

Roots

Answer 9

Common ancestors to the whole tree, link to rest of life

Question 10

Homology vs. Analogy

Answer 10

Homologous: shared by two or more species because they inherited this trait from a common ancestor.
Analogous: due to convergent evolution.

Question 11

Divergent vs. Convergent evolution

Answer 11

Divergent: related species evolve from a common ancestor and accumulate distinct differences where they become different species.

Convergent: different organisms/species develop similar traits from having to adapt to similar environments.
- Ex: the thunniform movement (motion is generated by moving the last third of the body), evolved via convergent evolution in tuna and sharks.

Question 12

Characters (phylogenetically informative characteristics)

Answer 12

Any observable characteristic

Question 13

Traits (or character states)

Answer 13

Character state, so a value
1) these observations of traits can infer patterns of ancestry and descent.
2) traits can be mapped to infer evolutionary events

Question 14

Monophyletic

Answer 14

• Common ancestor and all descendents
• a taxonomic group consisting of all descendants of the groups most recent common ancestor and no others.

Question 15

Paraphyletic

Answer 15

(of a group of organisms) descended from a common evolutionary ancestor or ancestral group, but not including all the descendant groups.

Question 16

Ingroup

Answer 16

the set of species that are more closely related to each other than to an outgroup.

Question 17

Outgroup

Answer 17

Group related but diverged earlier (helps in rooting)

Question 18

Sister taxa

Answer 18

Taxa from the same node

Question 19

Clade

Answer 19

Group of organisms that share a common ancestor

Question 20

Polytomy

Answer 20

Node with more than two organisms

Question 21

Carolus Linnaeus and Willi Henning

Answer 21

Carolus Linnaeus- original name is Carl Linne. He named a large amount of species and changed his name to be more Latin.

Willi- he was the founder of phylogenetic systematics.

Question 22

Vestigial Organs – why?

Answer 22

1) not selected against, not causing harm.
2) some natural selection against, natural selection is weak but it will be lost eventually.
3) the trait is disadvantageous but there is no ready path for natural selection to remove it.
4) the trait linked to a second trait that is being selected for
5) the trait has a function we have not found.

Question 23

Vertebrates and Tetrapod Tree (Which Vert groups are monophyletic which are not)

Answer 23

• Tetrapod vertebrates is a monophyletic group because it includes all descendants of the common ancestor of its members.
• Fish is paraphyletic group because it does not include all descendants of the common ancestor of its members.
• Dolphins are not monophyletic, because they are considered whales rather than dolphins.

Question 24

Aposematic Frogs

Answer 24

The coloration of the frogs is homoplasy! The coloration trait was so strong it evolved multiple times (convergent evolution).

Question 25

The examples of Homology vs. Analogy (Homoplasy) examples

Answer 25

Homology: wings of butterflies and moth Analogy: endothermy in birds and mammals

Question 26

Synapomorphy – Shared Derived Traits

Answer 26

A derived or "new" character trait shared by two or more taxa (groups of organisms) and their most recent common ancestor.

Question 27

Homologous Trait

Answer 27

A trait that is shared by two or more species because it has been inherited from a DA. (Wings of butterflies and moths).

Question 28

Homoplasy

Answer 28

a biological trait or structure shared by different species that was not inherited from a common ancestor (wings of moths and hummingbirds).

Question 29

Paraphyletic Pachyderms, Paraphyletic Birds of Prey

Answer 29

They are polyphyletic - groups that do not represent evolutionary clades (they're all over the tree).

Question 30

Sequence Alignment

Answer 30

Compares sequences to identify similarities and differences.

Question 31

Phylogeography

Answer 31

How a group of populations or species moved across the globe over the course of their evolutionary history.

Question 32

Parismony

Answer 32

The best phylogeny is the one that explains the observed character and data and posits the fewest evolutionary changes.

Question 33

Benghazi aid workers

Answer 33

- HIV breakout in Lybia - Some overseas workers were blamed and killed (Bulgarian) - This tree shows that it was impossible for these aid workers to transmit HIV (shows the origin of the spread) - They were sent back to Belgium

Question 34

Maximum Likelihood (Stats and Models)

Answer 34

Statistical method long before it was used as a phylogenetic search criterion.

Question 35

Bayesian Analysis/Inference (Stats and Models)

Answer 35

employs Markov chain Monte Carlo (MCMC) statistic to evaluate trees.

Question 36

What are both Maximum Likelihood and Bayesian Analysis/ what do they use?

Answer 36

- Both are statistical algorithms - Both use model of evolution

Question 37

Bootstrap resampling

Answer 37

looks at all data and randomly resamples, redoes analysis and tells you how often that clade shows up in the tree.

Question 38

Phylogenetic Distance Methods

Answer 38

Used for quick analysis

Question 39

Model of Evolution (Transitions vs. Transversions)

Answer 39

Models of molecular evolution distinguish between transitions (purine-to-purine A <--> G, or pyrimidine-to-pyrimidine C <--> T) and transversions (purine-to-pyrimidine, or vice versa)

Question 40

Heuristic Search

Answer 40

- a way to find shortcuts/ to eliminate lots of trees

Question 41

Microevolutionary Processes

Answer 41

migration and dispersal

Question 42

Macroevolutionary Processes

Answer 42

radiations and speciation

Question 43

Independent Contrasts

Answer 43

statistical method used in evolutionary biology to analyze trait data across species while correcting for their shared ancestry

Question 44

Polarity and outgroups

Answer 44

The determination of which character state is ancestral (older) and which is derived (newer) in evolutionary trees.

Question 45

Magpies and Phylogeography

Answer 45

Due to phylogeography, we can see how black beaks originated independently (how it was the ancestral color) compared to yellow beaks that originated much later (proving yellow was not an original color).