Evolutionary Trees Flashcards
define phylogeny
the evolutionary history of a species or group of species
define phylogenetic tree
a branching diagram representing a hypothesis about the evolutionary history of a group of organisms
define transitions (evolutionary modifications)
- hatch marks on the tree
- indicates the evolution of a trait at a particular point in an evolutionary lineage
what is the principle of parsimony
- used to determine which branching pattern is most likely
- parsimony = fewest steps or changes
define sister species
- species that share a more recent last common ancestor with each other than either shares with any other species
- they are each other’s closest living relatives
nuances on reading a tree - does adding a relationship change how the other’s are read?
no
nuances on reading a tree - how do you read time?
through branch length
nuances on reading a tree - how do you know if one species is more closely related to another?
- look at time
- not at branching points
define monophyletic clade
consists of an ancestral species and ALL of its descendants
define paraphyletic grouping
consists of an ancestral species and some NOT ALL of its descendants
define polyphyletic grouping
common ancestor of members is NOT part of the group
define polytomy
unresolved grouping where we do not know the correct relationships, so we cannot get the tree down to sister taxa
where would you see a sister taxon’s unique evolutionary history on a tree?
the branch after the node to the particular species
where would you see a sister taxon’s shared evolutionary history on a tree?
the branch before the node
where is a speciation event of a taxa located
the node connecting the taxa
where is the ancestral lineage of a taxa located
the line under the node that connects the taxa
what is the goal of phylogenetic reconstruction
identify monophyletic groups
explain the logic of a phylogeny inference under ideal conditions
- traits of the common ancestor are known
- evolutionary novelties evolve only once and are never lost in a lineage
- therefore, novelties can be interpreted as evidence of common ancestry
phylogeny inference under ideal conditions - what are the steps
- determine which novel traits are unique to a species and which novel traits are shared
- start drawing the tree from the tips and work back in time
- keep working back in time until all traits are nested
what do homologous characteristics form on a tree and why?
- nested pattern
- bc all life shares some traits and each successive smaller group of descendant organisms adds its own homologies to those it shares with larger groups
what is the outgroup comparison
used by systematics to differentiate between shared derived and shared primitive characteristics
what is an outgroup
- a species or group of species that is closely related to the ingroup (species we wish to infer)
- should be relatives of the ingroup but less closely related to them than the ingroup are to each other
- ensures that group will be monophyletic
outgroup comparison - what assumption is it based on
the assumption that homologies present in both the outgroup and the ingroup must be primitive characters
define homoplasies
- similarity in character states due to convergence and/or reversal
- aka analogous (opposite of homology)
- misleading info when estimating phylogenies
homoplasies - why do they occur
- convergent evolution
- when similar environmental conditions and natural selection produce similar adaptations in organisms from different evolutionary lineages
define apomorphies
an evolutionary novelty, or derived character
define pleisiomorphies
a preexisting, or ancestral character
define synapomorphies
- homologous traits that are shared and derived
- reliable info when estimating phylogenies
how can we maximize the use of reliable info when estimating phylogenies
using outgroups and parsimony
how do we reconstruct evolutionary history using sequence data?
- align the sequences
- then treat each site within a DNA sequence as a homologous character
reconstructing evolutionary history using sequence data - what does ‘treat each site as a homologous character’ mean
shifting to account for any insertions or deletions that have occurred in some lineages but not in others
reconstructing evolutionary history using sequence data - how to estimate evolutionary trees
- treat each site in a sequence as an independent character and look for synapomorphies that identify monophyletic groups
- then build trees using the variable location in the genome
- then identify transitions
reconstructing evolutionary history using sequence data - maximum likelihood
uses mathematical models of base pair substitutions to assess the probability of a given tree
reconstructing evolutionary history using sequence data: maximum likelihood - explain the branch length
- branch length is proportional to the number of nucleotide substitutions per site estimated to have occurred on each branch (not time)
- branch length and expected number of substitutions are based on the models of sequence evolution and the actual DNA sequence data
reconstructing evolutionary history using sequence data: maximum likelihood - how do you determine which is the maximum likelihood
- sum the probabilities at every nucleotide for every tree
- max one is maximum likelihood
reconstructing evolutionary history using sequence data - bootstrapping
- used after using maximum likelihood method to measure sure you’re confident that you are correct
- it generates random data sets by random sampling
reconstructing evolutionary history using sequence data: bootstrapping - how does it work?
- it randomly choses numbers 1-6 representing nucleotides
- it will then randomly pick a site and does this repeatedly to make a bootstrap replicate and make a tree
- it will calculate a majority rule consensus
