Evolution Lecture 6

Question 1

Systematics

Answer 1

The study of the diversity of life. A discipline focused on classifying organisms and determining their evolutionary relationships.

Question 2

The two types of systematics?

Answer 2

Taxonomy and Phylogenetics

Question 3

Taxonomy

Answer 3

Naming & identification of taxa: Species and groups of species. Created by Linnaeus, he proposed we should have hierarchical nested taxonomy. As the groups go into another group, you get more species and it’s more general. However, it doesn’t tell us anything about the relationship.

Question 4

Taxa

Answer 4

Named unit at any level of the hierarchy. (eg. order, class, kingdom).

Question 5

Order of the taxa (from most general to specific)?

Answer 5

Domain, kingdom, Phylum, Class, Order, Family, Genus, Species.

Question 6

Binomial Nomenclature

Answer 6

A two word name created by Linnaeus, so every organism can have a unique name, so that all scientists can understand it. The first word is the genus it’s assigned to, and the next word is the specific epithet (it’s one of a kind). Everything is capitalized but the species. Genus and species epithet are italicized. The species group is two words and the rest is one.

Question 7

Phylogenetics

Answer 7

Estimation of evolutionary trees (‘phylogenetic trees’ / ‘phylogenies’). Shows the relationship of species (things that could have evolved). Uses homologies.

Question 8

Morphological Characteristics

Answer 8

Physical features. Eg. Size, shape, and anatomical features.

Question 9

Taxonomy and Phylogeny?

Answer 9

Hierarchical nested taxonomy is consistent with a tree-of-life. Most biologists today consider that
taxonomy should reflect phylogeny specifically, taxa should be monophyletic groups where possible.

Question 10

Parts of a phylogenetic tree?

Answer 10

Branch (connected a ancestor to its descendant)

Branch Point (Internal nodes, they are a common ancestor and where a speciation event occurred)

Tips (Terminal nodes, living species typically)

Sister Taxa (The descendants that are the most related)

Basal Taxon (A lineage that diverges from all other members of its group early in the history if the group).

Question 11

Can the trees be drawn in different ways?

Answer 11

Yes, ‘Rotating’ the nodes doesn’t change the meaning. Or if you draw it using different lines. Drawing it depending on what’s convenient for you. But if you cut a branch and put it somewheres else completely it will be different.

Question 12

Do we usually label the internal nodes?

Answer 12

No

Question 13

Cladogram

Answer 13

Branch lengths have no particular meaning.

Question 14

Phylogram

Answer 14

Branch lengths represent (inferred) amount of evolutionary change [Especially used for molecular
phylogenies - more later]. Longest line has the most evolutionary change.

Question 15

Monophyletic group (Clade)

Answer 15

Groups that includes an ancestral species and all of its descendants. (eg. plantae which are land plants)

Question 16

Paraphyletic group

Answer 16

An ancestor and some, but not all, of its descendants.

Question 17

Polyphyletic group

Answer 17

A group that does not include its own most recent common ancestor (= 2+ branches artificially grouped together).

Question 18

How long have scientists been proposing taxa?

Answer 18

150 years

Question 19

Reptiles example?

Answer 19

Dinosaurs and bird create a paraphyletic group. WE also have to look at the fossil record to determine the tree.

Question 20

How to fix reptiles to become a monophyletic group?

Answer 20

Live with it

Break it up into smaller monophyletic groups

Include birds has reptiles

Question 21

Ratites Example?

Answer 21

A polyphyletic group (birds that can’t fly). It independently (convergent) lost the ability to fly.

Question 22

How do we infer phylogenies?

Answer 22

Character states (possible homologies): Morphological features, etc. Identities in DNA / protein sequence. Where we see different versions of something in the same tree. If they share it probably closely related.

Distribution of character states among
organisms reflect evolutionary relationships

Question 23

Derived and ancestral characteristics?

Answer 23

The original state in the ancestral is ancestral (0) and the one that’s new is not, which is derived (1). It’s evolutionary novelty unique to a clade.

Question 24

Cladistic reasoning?

Answer 24

Shared derived states imply relationships. Shared ancestral states do not. Outgroup comparison (usually) to distinguish ancestral and derived states (a species you know is quite distantly related and has the ancestral state).

Question 25

Complex structures in phylogenetics?

Answer 25

The more elements similar in complex structures the more likely they evolved from the same common ancestor.

Question 26

Expression of uncertainty in the trees?

Answer 26

Where they come to a point because we don’t know which one branched off first.

Question 27

Cladistics

Answer 27

Example multiple characteristics at once using a character table.

Question 28

What has the most derived characters?

Answer 28

The one farthest from the ancestor.

Question 29

Clastistic Reasoning

Answer 29

Inferring evolutionary relationships from the character states of a series of characters.

Question 30

What if character state distributions NOT all consistent with same tree?

Answer 30

Due to
– Convergent evolution (something similar evolved twice or more on the tress of life, because of similar environmental pressures).
– ‘Reversals’ (e.g. loss of derived state; 1 to 0)

One method – Parsimony:
* Compare many (all) possible trees:
* Best inference is the tree that implies fewest evolutionary changes total.

Question 31

Clades on parsimony?

Answer 31

Have only one change, it’s not a clade if it has more than one.

Question 32

What dinosaurs are closer to birds based on parsimony?

Answer 32

The lizard hipped, not the bird hipped.

Question 33

Can reversal be better?

Answer 33

The most parsimonious history for a character might involve ‘reversal’ rather than convergence.

Question 34

Molecular Sequence data

Answer 34

Phylogenies of living taxa usually estimated by comparing molecular sequences (e.g. DNA or animo acids), and they don’t have to code something. A site in a set of aligned DNA sequences is a character: Different bases at site are the states. Comparing the same nucleotide of the same gene. Aligned is important to make sure we are comparing the right things.

Question 35

What does a dashed line in Molecular Sequence data mean?

Answer 35

A nucleotide is missing. If it wasn’t there the table would look a lot different. A mutation occurred, deletion.

Question 36

Molecular Homoplasis

Answer 36

Organisms that don’t appear to be closely related, the bases the their otherwise very different sequences happen to share may simple be coincidental matches.

Question 37

Maximum Likelihood

Answer 37

Identifies the tree most likely yo have produced a given set of DNA data, based on certain probability rules about how DNA sequence change over time.

Question 38

What do most analyses use?

Answer 38

Use models of sequence evolution (rather than parsimony). Model may reflect the fact that transitions (C to T and A to G) occur more frequently than transversions.

Question 39

When we compare the entire genomes of different organisms what do we see?

Answer 39

Lineages that diverged long ago often share many orthologous genes. The # of genes a species has doesn’t seem to increase through duplication at the same rate as perceived phenotype complexes.

Question 40

How to find the evolution of a gene?

Answer 40

Molecular sequencing. The evolution could be different than the history of the gene.

Question 41

Phylogenies of genes?

Answer 41

Evolution of genes themselves often of interest. e.g. tracing history of gene duplication, or of gene transfer between genomes. One of many aspects of the disciplines of molecular evolution and genome evolution.

Question 42

Lateral/Horizontal Gene Transfer

Answer 42

Transfer of a few genes between very distantly related species. Quite common in unicellular organisms. It happens when a cell dies and explodes and chunks of DNA are floating around then get incorporated into a new species, and the species could change.

Question 43

What diverged first?

Answer 43

Bacteria

Question 44

How to figure our which group donated this ‘bacterial’
gene to an ancestor of these amoebae?

Answer 44

Get gene sequence from each and compare.