Lecture 3: Phylogeny, Tree of Life, Taxonomy and Systematics Flashcards
Taxonomy
the science of describing, naming, and classifying organisms
Taxon (plural = taxa)
a unit of taxonomic classification
Systematics
the study of biological diversity and the evolutionary relationships among organisms
What types of hypotheses can be tested with systematics?
Hypotheses about which groups have descended from a common ancestor
Extinct
no longer present
Extant
taxa that exist today
Phylogeny
the history of descent of a group of taxa from their common ancestors
What is used to depict phylogenies?
Phylogenetic trees
Phylogenetic hierarchy
Kingdom, Phylum, Class, Order, Family, Genus, Species
(King Philip Came Over For Good Soup)
3 Domain System
Eukayra (multicellular eukaryotes)
Bacteria (prokaryotes)
Archaea (single celled prokaryotes)
Who introduced binomial nomenclature?
Carl Linnaeus
What are the two parts of binomial nomenclature?
Genus and species
Ex: Megacephala virginica
What do the tips of a phylogenetic tree represent?
Taxa
Root
Common ancestor of all taxa
Node
A branchpoint in a tree
Clade
A group of two or more taxa that includes both their common ancestor and all their descendents
Common ancestor
Ancestor shared by 2+ individuals
Monophyletic group
A clade. A group that includes all of the descendents of a common ancestor
What is a trick to see if a group is monophyletic?
Rotate the node and see if the taxa stay in the same box
How can you tell which species are closely related on a phylogenetic tree?
Species that share a more recent common ancestor are more closely related
Paraphyletic group
A group that includes some, but not all descendants of a common ancestor
Polyphyletic group
A group that consists of members of multiple lineages but does not consist of the most recent common ancestor and all of its descendents
Character
A particular trait of interest
Homologous characters
Characters that a given set of organisms have inherited from their common ancestor
Character state
A given character can have many different character states
Ex: 5 digits on forelimb, one digit on forelimb
Ingroup
The group of interest, usually assumed to be monophyletic with respect to an outgroup
Outgroup
A group of taxon that is related to the ingroup
Steps
The number of inferred changes in character state on a tree
Most parsimonious tree
The tree with the shortest number of steps/changes
Plesiomorphy
Ancestral character state
Symplesiomorphy
Shared ancestral characters, not phylogenetically informative
Apomorphy
Derived character state
Synapomorphy
Shared derived character, most useful for inferring phylogenetic relationships
Autapomorphy
Unique derived character state, not useful for inferring relationships, but helpful for identification of species
Occam’s razor, related to Parsimony
Among competing hypotheses, the one with the fewest assumptions should be selected
Topology
Pattern of branching
Two methods for dealing with long branches
Maximum Likelihood and Bayesian
Maximum Likelihood
Calculate the likelihood of observing the data
Bayesian
Maximizes the probability of observing a tree
Maximum likelihood vs Bayesian
ML calculates likelihood of observing a possible tree, Bayesian provides probability of multiple trees
Long branch attraction
Just by chance, two long branches will have the same change at some nucleotide positions. These branches are attracted to each other in a parsimony analysis
Gene tree
A phylogeny of alleles/genes for a specified stretch of DNA
What are orthologous genes?
Genes that descended from the same locus in their most recent ancestor (a1 and a2, b1 and b2)
What are paralogous genes?
Genes that arise via ancestral gene duplication
(a1 and b1, a2 and b2)
Which of the following is more closely related:
- orthologous loci in different species
- paralogous loci within the same species
Orthologous loci in different species
What is an example of an ancestral character state
Opposable vs non-opposable foot/thumb
What can the Molecular Clock be used for
To calibrate evolutionary trees to absolute time
Homology
Features inherited from common ancestors. Ex: birds, bats, mice, and crocodiles all have four limbs
Homoplasy
Independent evolution of a character or character state on a phylogenetic tree
Convergent evolution (convergence)
Organisms independently evolve similar traits
Parallel evolution (parallelism)
Two species that have descended from the same ancestor remain similar over time
Evolutionary reversal
Return from an advanced to a more primitive character
Does branch length impact patterns of evolutionary decent?
no it is the same regardless of branch length
Does rotating branches change relationships on a phylogenetic tree?
no
