Lecture 8: Phylogenetics

what is phylogenetics

The study and reconstruction of evolutionary relationships among organisms

what is a phylogenetic tree

A model or hypothesis representing evolutionary relationships and ancestry among taxa

why are phylogenetic trees considered hypotheses rather than facts

Evolutionary history cannot be directly observed, so trees are inferred from evidence

what types of characteristics have traditionally been used to reconstruct phylogenies

Morphology, paleontology, and geography

what are cryptic species

Distinct species that are difficult or impossible to distinguish using traditional morphology

what is convergent evolution

The independent evolution of similar traits in different evolutionary lineages

why is DNA useful for molecular phylogenetics

DNA sequences can be compared among organisms, evolve in measurable ways, provide many characters, and can clarify difficult evolutionary relationships

what is molecular phylogenetics

Reconstructing evolutionary relationships using molecular data such as DNA sequences

what does a node represent on a phylogenetic tree

an inferred common ancestor and divergence event

what does a branch represent

A relationship among taxa in terms of descent and ancestry

what is topology

The branching pattern of a phylogenetic tree

what does branch length represent

The amount of evolutionary change that has occurred along the branch when the tree is scaled for change

what is the root of a phylogenetic tree

The inferred common ancestor of all taxa in the tree

what is an unrooted tree

A tree showing relative relationships among taxa without identifying a common ancestor or direction of evolution

what is a rooted tree

A tree that identifies a common ancestor and allows the direction of evolutionary relationships to be interpreted

what is a clade

A group containing a common ancestor and all of its descendants

what is an OTU (Operational Taxonomic Unit)

The taxonomic level selected for sampling in a phylogenetic analysis; it can be an individual, population, species, genus, or other group

what is a distance scale on a phylogenetic tree

A scale representing the number of differences between organisms or sequences

what is an outgroup

A taxon less closely related to the focal group than the focal taxa are to one another

why is an outgroup used

To establish the root of the tree and help determine the evolutionary pathway

what is nonophyly

A group containing an ancestor and all of its descendants

what is paraphyly

A group containing an ancestor and some, but not all, of its descendants

what is a polyphyly

A group combining organisms from different evolutionary lineages

what are the four steps of phylogenetic analysis

Align sequences, determine the substitution model, build the tree, and evaluate the tree

what is sequence alignment

Arranging homologous DNA or amino acid sequences so corresponding characters can be compared

why are gaps sometimes added during sequence alignment

To account for insertions and deletions and align homologous positions

what are the three basic types of sequence mutation emphasized in the phylogenetic analysis

Substitution, insertion, and deletion

what is a transition

A substitution between two purines (A↔G) or two pyrimidines (C↔T)

what is a transversion

A substitution between a purine and a pyrimidine

which generally occurs more frequently, transitions or transversions

Transitions are generally more likely because of structural similarity between the bases

what is the jukes-cantor model

A basic nucleotide substitution model that assumes all nucleotide substitutions occur at equal frequencies

what is the kimura two-parameter model

A substitution model that allows transitions and transversions to occur at different rates

what are the four major approaches to tree building

Distance, parsimony, maximum likelihood, and Bayesian inference

what is the basic idea of the distance method

Convert sequence differences into pairwise distances and find the tree that best represents those distances

what is the basic idea of parsimony

Prefer the simplest evolutionary explanation requiring the fewest character-state changes

what is maximum likelihood

Find the tree/model with the highest probability of producing the observed data

what is bayesian inference

Estimate the probabilities of trees given the observed data and identify trees with the highest posterior probability

what is bootstrap analysis

Randomly resampling the data with replacement, rebuilding trees repeatedly, and determining how often particular clades occur

what does a bootstrap value represent

The proportion of resampled trees that contain a particular clade

what is a bayesian posterior distribution used for in phylogenetics

Determining the fraction/proportion of simulated trees that contain a particular clade

what is the difference between a bootstrap value and bayesian posterior probability

Bootstrap evaluates clade support through repeated resampling, whereas Bayesian posterior probability reflects the proportion of simulated trees supporting the clade under the Bayesian model

what can phylogenetic reveal about geography

It can show the spatial distribution of evolutionary lineages and help determine how landscape history may have influenced evolution

what is phylogeography

The study of the geographic distribution of genetic lineages and its relationship to evolutionary history

how can phylogenetics help define management units

It can identify populations that are evolutionarily, geographically, or adaptively distinct and may therefore require different management strategies

what is a host-parasite phylogeny used to investigate

The evolutionary relationships between hosts and their parasites

are host and parasite evolutionary histories always perfectly linked

No. Their evolution is linked imperfectly

how can phylogenetics be applied to conservation

It can identify distinct evolutionary lineages and help prioritize populations or lineages for conservation

why might older lineages with deeper evolutionary splits recieve conservation priority

They represent greater evolutionary distinctiveness

does every gene necessarily produce the same phylogenetic pattern

No. Different genes can have different evolutionary histories

How does molecular phylogenetics complement population-structure approaches

Population structure is useful for more recent genetic divergence among groups, while phylogenetic methods are generally applied when greater evolutionary divergence is expected