Lecture 4 (phylogeny)

Question 1

Define a taxonomy and describe its similarity and difference with systematics

Answer 1

Taxonomy:
-Classifying species based on similarities and differences
-Quite generalized
-Does not explain evolutionary relationships

Systematics:
-Explains evolutionary relationships based on phylogeny (cladistics and phylogenetics)
-Organizes biological diversity and explains evolutionary events like speciation

Question 2

Explain what a phylogenetic tree is

Answer 2

-Shows evolutionary relationships with ancestors and descendants
-Consists of a root, basal taxon, nodes, sister taxa, polytomies, and tips
-Created via homologous traits, morphological and molecular data
-They are hypotheses so they’re tested and repeatedly modified
-Strongest evidence is by looking at common ancestry

Question 3

Explain what morphological data is

Answer 3

-Compares size, shape, # of bones, and anatomical similarities and differences
-For extinct and extant species

Question 4

Explain what molecular data is

Answer 4

-Compares DNA, RNA, and Nucleic acids to recognize similar characteristics amongst species that cannot be determined by morphological data
-Helped determine three main domains and therefore affected taxonomic classifications
-For extant species

Question 5

Define the following terms that are involved in phylogenetic trees

Answer 5

Taxa: individual organisms, species, or a group of species

Node: A branch point that depicts a common ancestor; can be rotated as it does not change relationship; do not count nodes

Sister Taxa: Two (or more ?? ask) taxa that share a common ancestor and are closely related

Basal Taxon: A species that diverged from the tree early on; its most recent ancestor is the root (Ask if this is always true)

Speciation: Evolutionary event; divergence from a common ancestor; more complex shared characteristics are, the more closely related

Root (ancestral lineage):The common ancestor for all taxons in the phylogenetic tree

Polytomy: When there are 3+ species stemming from a single common ancestor

Tips: Also known as the descendant taxa; represents a group of taxa (a clade) or a taxon

Lineage: Path of evolution for an ancestor and its descendants

Question 6

What does branching tell you in phylogenetic trees

Answer 6

-The amount of time that has passed before speciation occurred
- The amount of evolutionary changes that occurred
DO NOT COUNT NODES AS THEY DON’T DEPICT THE ORDER IN WHICH THE SPECIES APPEARED UNLESS THEY FOLLOW THE SAME PATH
-The further away taxa are at the tips, the larger the changes that they underwent; sister taxa undergo minimal changes
-The trees don’t show evolutionary advancement in terms of placement as this idea does not exist

Question 7

How do polytomies arise

Answer 7

-Lack of knowledge; further research is made (collection of morphological and molecular data) until a differentiation can be made
-Rapid speciation occurred which led to minimal changes amongst taxa

Question 8

Which method is the most ideal to track evolutionary relationships: Morphological data, molecular data, or both

Answer 8

-Individually, molecular as it shows relatedness that cannot be seen by naked eye
-But ideally both methods are used

Question 9

How does taxonomy and phylogeny (cladistics) relate

Answer 9

-All clades are taxa but not all taxa are clades
-Shows that there is an inconsistency in taxonomy
-Why phylogeny is more accurate in comparing species

Question 10

Define homology

Answer 10

-Similar characteristics stem from common ancestor
-Phylogenetic trees are built off of homologous traits
-Shared characteristics tend to be more complex as it proves that there are close similarities in molecular and morphological data which is where the importance of complexity comes from

Question 11

Define analogy and homoplasy

Answer 11

-Shared characteristics are not derived from same ancestor
-Traits evolved independently
-Arrived due to similar environmental conditions
-Species are not closely related
-Shared characteristics are very simple

Homoplasy is another term for an analogous structure.

Question 12

What is convergent evolution

Answer 12

-Independant evolution of similar traits in different lineages

Question 13

Define an ingroup and its relation to an outgroup

Answer 13

Ingroup: the group of taxa that you want to study

Outgroup: One or more taxa that is related to the ingroup by diverged early on

Question 14

What are characters

Answer 14

-Anatomical, physiological, or molecular features of organisms

-Character states are the presence or absence of characteristics

Question 15

Shared derived character vs. Shared ancestral character

Answer 15

Shared derived characteristics (Synapomorphy):
-A shared trait between two or more taxa and their most recent common ancestor but is not found in the ancestor that precedes the clade

Shared ancestral character (symplesiomorphy):
-A shared trait between two or more taxa including the preceding ancestor of the clade

Question 16

Define apomorphy and which term it is correlated to

Answer 16

-A derived character
-Correlated with synapomorphy

Question 17

Define Plesiomorphy and its relation to symplesiomorphy

Answer 17

-An ancestral character
-Correlated with symplesiomorphy

Question 18

Define a clade and a nested hierarchy

Answer 18

-Consists of an ancestor and its descendants
-All clades are taxa but not all taxa are clades due to the lack of specification and accuracy in relation w.r.t. evolution
-A nested hierarchy explains how clades can grow in size as you include more ancestors and all their ancestors

Question 19

How are clades simplified

Answer 19

If you have a clade that has a number of descendants of the same ancestor, it can be collapsed into showing just the common ancestor

Question 20

How do cladograms compare and differ to phylogenetic trees

Answer 20

Similarities:
-Both depict evolutionary changes

Differences:
-Cladograms only show the evolutionary relationships; branch length holds no significance

Question 21

What is cladistics

Answer 21

-Looking at homologous characteristics (phylogeny) to understand evolutionary relationships

Question 22

Define monophyletic

Answer 22

-Also known as a clade
-Consists of an ancestor taxon, all its descendants, and no unrelated taxa

Question 23

Define paraphyletic

Answer 23

-Consists of an ancestral taxon but not all of its descendants

Question 24

Define polyphyletic and how its derived

Answer 24

-Includes distantly related taxa (shared ancestor but not recent), but does not include most common ancestor for entire group

-Incorrect taxonomic classification (can be easily fixed but stemmed from forming tree via generalized similarities and not specific similarities)
-The group is missing common ancestor that unites them all (missing fossil records)
-Have more than one common ancestor due to speciation

Question 25

Check to see if you need to learn how to build a cladogram/ phylogenetic tree