Classification, phylogeny, and systematics Flashcards
How were organisms classified before Darwin?
Kinds, types, ideals (Scala naturae), similarities, characteristic features
How were organisms classified after Darwin?
Shared ancestry, phylogeny, adaptations
How do we know all life originated from a single common ancestor?
DNA evidence, all life has DNA, suggesting it originated before domain Bacteria spilt off
What is LUCA?
Last universal common ancestor
How is Linnean taxonomy hierarchal?
Starts with the most inclusive categories and gets more exclusive
What levels of classification did Linneaus have?
Kingdom, phylum, subphylum, class, order, family, genus, species
How many levels of classification do we have now?
35-37
What is systematics?
Study of evolutionary relationships
What does systematics do?
Reconstructs patterns of relationships between species, who shares common ancestors and builds classifications based on the patterns. It tries to establish phylogenies
Who was Willi Hennig? What did he do?
Developed the idea of phylogenetic systematics
What 3 things were important when creating a phylogeny according to Willi Hennig?
Genealogical relationships, synapomorphies, and the taxonomy needs to be logically consistent with what is believed to be the pattern of historical relationship
What is the difference between an ancestral and derived character state?
An ancestral character state was found in the ancestor, so is more primitive. Derived states are not seen in the ancestor
What is a pleisiomorphy?
An ancestral character state
What is a symplesiomorphy?
A shared ancestral character state
What is an apomorphy?
A derived character state
What is a synapomorphy?
A shared derived character state
Between pleisiomorphies, sympleisiomorphies, apomorphies, and synapomorphies, which one is most important for systematics?
Synapomorphies
What is the difference between a character and a character state?
A character is the characteristic of an organism with variable features. A character state is alternate conditions of a feature, like something present or absent
What characters are examined when determining phylogenies?
Characters that reveal evolutionary relationships without being too common
Why do we want a character to have two character states when determining phylogenies?
Much easier to plug into a computer as 0 and 1
What is homology?
Similarities because of shared ancestry, doesn’t need to have the same function
What is analogy?
Similarities because of similar function and not common ancestry
What is convergent evolution? Is it homology or analogy?
Organisms from different ancestries converged onto similar habitats and developed similar traits as a result. It is analogy
What is parallelism?
Independent evolution of a similar structure in related groups, but that trait was not passed down from the most recent common ancestor
What is a monophyletic group?
Taxon/group that includes the most recent common ancestor and all its descendants
What is a polyphyletic group?
Taxon/group that includes members from two or more ancestors
Which of the original 5 kingdoms was a polyphyletic group?
Protista
What is a paraphyletic group?
Taxon/group that includes the most recent common ancestor but not all of its descendants
What is an evolutionary tree? What is on the x and y axises ?
Plots time on the y-axis and genetic divergence on the x-axis
What is the difference between an evolutionary tree and a phylogenetic tree/cladogram?
Evolutionary trees recognize paraphyletic groups, while phylogenetic trees only recognize monophyletic groups
What is the operational taxonomic unit?
The taxonomic level of sampling used in a study that is selected by the researcher
What is a clade?
A group of 2 or more taxa that includes the most recent common ancestor and all its descendants
What is a node?
A branch point in a cladogram
What is a branch?
Represents a lineage, the relationship between taxa and their descent and ancestry
What is topology?
The branching pattern of the tree
What is the branch length?
The number of changes in characters that occurred on the branch
What is the root?
The common ancestor of all OTUs on the cladogram
What is a sister group?
Two clades that split off from a single lineage
What is the terminal node?
The terminal taxa at the end of the cladogram
What is an internal node?
A branch point that represents a common ancestor
How can we use phylogenetic trees to get an idea of the rate of evolution?
Look at the branch length, how many characters have changed since diverging off from the common ancestor
If two species that diverged off from the same ancestor evolve at different rates, are they still sister groups?
Yes, because they branched off from the same ancestor
How do we know when a species is evolving fast or slow?
More character changes means faster evolution
What are homoplasies? What are the two types?
Shared features that aren’t homologies. Evolutionary reversals and convergences
What is an evolutionary reversal?
The reversion of a character state from derived back to ancestral
What is convergence?
Independent origin of apomorphies in 2 or more taxa
What is parsimony?
The tree with the fewest evolutionary changes is the best one
Why the shortest phylogenetic tree the most likely and best tree?
It minimizes the number of hypotheses required to explain it
What is an outgroup?
A group that is a close relative to the group of interest that isn’t being studied itself
What is the ingroup?
What is being studied
Why is an outgroup useful when building a phylogenetic tree?
It indicates the direction of evolutionary change and which character states are primitive and derived
What makes the best outgroup?
The sister group to the ingroup
What is phylogenetic tree rooting?
Defining the position of the hypothetical ancestor of the groups on that phylogenetic tree
What information does an unrooted tree not tell us?
The direction of evolution
What is midpoint rooting?
The root is in the middle of the two most distantly related species
What is outgroup rooting?
The root is placed so the outgroup is the first to diverge off, shows time-directed evolutionary history
What are the steps for creating a cladogram with maximum parsimony?
- select ingroup species
- select one or more outgroup species
- Determine the polarity of many different characters in the outgroup and all the ingroup species (pleisiomorphic or apomorphic)
- Draw unrooted trees with all species that plot the changes in all characters
- Choose the most parsimonious tree
- Root the tree between the outgroup and the ingroup
What is a gene tree?
A branching diagram of the history of a DNA sequence - haplotypes. A phylogenetic tree of genetic information
Why are haplotypes (DNA sequences) more similar among organisms in the same region?
Being in the same region increases interbreeding, and less likely to interbreed with other populations
What are pseudogenes? Are they affected by natural selection?
Sections of DNA that don’t encode anything. They aren’t affected by natural selection
What is a molecular clock?
An estimation of the time at which a lineage diverged
What regions of the DNA do molecular clocks examine?
Non coding DNA. It isn’t affected by natural selection, so it probably has a clock-like rate of change
Why does the rate of change of a DNA sequence remain relatively constant?
Changes in non coding regions and silent mutations don’t show up in the phenotype and aren’t affected by natural selection, so they accumulate at a stochastic rate
Why doesn’t the rate of change of a DNA sequence always remain constant?
Rates are different from one taxonomic group to another, and molecular clocks are estimates only
