Evolution: Lecture 6 Flashcards
What is systematics?
The study if the diversity of life. Trying to work out all our information about it.
What are the two components of systematics?
Taxonomy and Phylogenetics
What is taxonomy?
Naming and identification of taxa: species and groups of species. The identification of taxa and categorization of taxa to house species.
- Family, orders, domains
What is phylogenetics?
An estimation of the influence of evolutionary trees (phylogenetic trees or phylogenies)
what are the taxa in increasing specificity?
Domain
Kingdom
Phylum
Class
Order
Family
Genus
Species
What are taxa?
They are groups of similarities between organisms. It is highly based on Linnaean evolution. Each taxa are groups of other (smaller) taxa.
What kind of name do we give spices?
Binomial nomenclature. Made up of genus and specific epithet.
Panthera pardus
Why do we use such unique names?
We use unique names that mean the same thing to all scientists. They would stay the same regardless of the language.
What supports taxonomy and phylogeny?
Hierarchical nested taxonomy is consistent with the tree of life. It is also the part of Linnaean’s ideas that worked well with Darwin’s ideas.
Biologists consider that?
Most biologists today consider that taxonomy should reflect phylogeny.
What are phylogenetic trees?
A branching tree diagram that communicates relationships between organisms/evolving things.
Tips and Branches and sister taxa?
- Tips are normally representative of living species
- Branch points or internal nodes represent the common ancestors
- Sister taxa are species that branch from the same ancestor
Cladogram?
A phylogenetic tree where branch lengths have no particular meaning.
Phylogram?
Where branch lengths represent inferred amount of evolutionary change or time.
- Very useful for molecular phylogenies.
Monophyletic group (clade)?
An ancestor and all of its descendants.
Example: snipping off a full branch
Paraphyletic group?
An ancestor and some, but not all, of its descendants
Example: snipping off a branch and getting rid of a twig on it
Polyphyletic group?
A group that does not include its own most recent common ancestor (= 2+ branches artificially grouped together)
Example: grabbing a bunch of twigs and holding them together like a branch
Many biologists also consider?
Taxonomy should reflect phylogeny and taxa should be monophyletic groups when possible.
How do we infer phylogenies?
Character states (possible homologies)
– Morphological features, etc.
– Identities in DNA / protein sequences
Distribution of character states among organisms reflect evolutionary relationships
What do we look at for the distribution of character states?
We look at the distribution (among organisms) of a characteristic by observing the different states of it.
Example: Non-retractable vs retractable claws.
What are the 2 options for a state of a character?
- There is the original (ancestral) state
- There was an evolutionary change where the ancestral state changed into a new one (derived state).
Shared derived states?
Imply relationships. Evidence that they are closer to each other than the ancestral states.
Shared ancestral states?
do not imply relationships.
What is the outgroup comparison?
Outgroup comparison (usually) to distinguish ancestral and derived states
How do we measure evolutionary change?
From ancestral to derived: 0-1
From derived to ancestral: 1-0
Derived = 1
Ancestral = 0
What is cladistics?
Cladistics is when we examine multiple characters and form a character matrix/table.
What is cladistic reasoning?
A way of inferring evolutionary relationships from the character states of a series of characters.
Why are character state distributions not all consistent with the same tree?
This could be due to:
- Convergent evolution. Traits evolve similarly on different parts of the tree. “analogy not homology”
- Reversals (loss of derived state 1-0)
What is parsimony?
- Compare many (all) possible trees:
- Best inference is the tree that implies fewest evolutionary changes total.
Molecular sequence data involves?
- Phylogenies of living taxa are usually estimated by comparing molecular sequences (e.g. DNA).
- A site in a set of aligned DNA sequences is a character: Different bases at site are the states
Molecular sequence table?
It is similar to the character table. We compare similar gene sequences in organisms. We try to have the same nucleotide sequence being compared.
Example with a gap in species Z?
There is a nucleotide missing. We can place a gap in the sequence to have the best fit possible. This is under the assumption that there was a possibility that Z had an event where a nucleotide was deleted.
- Information is inferred by the scientist for the best fit.
Morphological character vs. site in DNA sequence?
0-1 would be c-t
Phylogenetic trees of molecular sequence analyses?
Most analyses use models of sequence evolution (rather than parsimony)
Example: Model may reflect the fact that transitions occur more frequently than transversions
Transition substitutions: common
C-T and G-A
Transversion substitutions:
G-T C-A G-C and T-A
Sars COV-2 (COVID-19)?
Shows us that there is proof that COVID-19 was related or is related to other viruses in bats. Therefore, we have a level of certainty that COVID descended from a bat virus.
Phylogenies of trees?
Evolution of genes themselves often of interest. Gene’s evolutionary history in genomes.
- 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
Lateral or Horizontal Gene Transfer?
Transfer of genes between species
* Quite common in unicellular organisms and plants
Where do we see this transfer?
Typically it is between distantly related species or those that aren’t related at all.
What is the result of the gene transfer?
The cell that received the segment will now express new genes. Ones that the ancestor would not have had.
