Phylogeny Flashcards
Give examples for the sorts of phenotypes you can use for phylogenetic analyses
Morphometric characters
DNA sequences
Protein sequences
Why is a fossil record extremely helpful for phylogenetic analyses if available?
Because it allows you to calibrate your phylogeny
What do you need to carry out phylogenetic analyses?
Phenotypes and characters
What phenotype characters would need to be aligned?
DNA and protein
Name a software that can carry out multiple alignments
CLUSTAL
When would you need to correct an alignment (that was generated by computer software) by eye?
If there is a repetitive element to the sequences
Is phylogeny done by hand or by computer?
Computer
There are many algorithms for generating phylogenies, give examples of some of the packages
PHYLIP
CLUSTAL
MEGA
List three methods used to generate phylogenetic trees
Parsimony methods
Distance methods
Maximum likelihood
Which method for generating phylogenetic trees is the most complicated?
Maximum likelihood
Give examples of some distance methods
UPGMA
Fitch-Margoliash
Neighbour joining
Distance Wagner
How do you know if a tree is reliable?
By using statistical analysis called ‘bootstrapping’
Does DNA and protein data give the phylogenetic relationship of the gene or the species?
Only the gene, not the species
Can different fragments of a gene or protein have different phylogeny? Why?
Yes
Because of natural selection
What is the best material for phylogeny based on molecular biology?
DNA that is evolving neutrally
E.g. junk DNA such as intergenic regions, introns, pseudogenes
(Mutation rate is clock-like)
Why is mitochondria often used as molecular material for phylogeny?
Because it is a small molecule that is easily isolated
Is the mitochondria inherited maternally or paternally?
Maternally
How much recombination happens in the DNA of the mitochondria?
None
How can you genotype mitochondrial DNA?
By PCR and sequencing
Is mitochondria selectively neutral?
Yes
What can Thr-Gly repeats be used for looking at the phylogeny of?
Closely related Drosophila species
For what type of phylogeny would you need to specify a model using rRNA?
Maximum likelihood
Is the parsimony method fast or expensive on computer time?
Very expensive
Is the maximum likelihood method fast or expensive on computer time?
Expensive
Are distance methods fast or expensive on computer time?
Fast
How can you improve the reliability of a phylogenetic analysis?
Use bootstrap
Use different algorithms
Build a consensus among the various methods
Usually one topology will predominate
Compare to other DNA sequences with the same species
Describe the Indo-west Pacific species of the fiddler crab (Uca)
Behaviourally simpler
More aquatic
How many species of the fiddler crab (Uca) are there?
Many
Describe the American species of the fiddler crab (Uca)
More terrestrial
More complex behaviourally and morphologically, e.g. mate guarding, displays etc.
For frogs and swordtails, is the sensory bias hypothesis supported or not?
Yes, with molecular phylogenies
Is the mitochondria a small or large molecule?
Small molecule
What is the size of the DNA of mitochondria?
~16500bp
How much of the mitochondrial sequence is known?
The entire sequence
Describe the mutation rate of mitochondria
High mutation rate, no DNA repair so very variable
What is the most variable part of the mitochondria?
The D-loop (control region)
What part of the mitochondrial DNA has a lack of functional constraints?
The D-loop
What does HVS stand for?
Hypervariable sequence
What do outgroups give to a tree?
Directionality
What happens to a tree when you add an outgroup?
The tree becomes rooted, as opposed to unrooted
If a particular species is closest to the outgroup, what is the term given to this species?
The ‘ancestral species’
What is meant by the ‘ancestral species’?
A species more similar to the real ancestor, even though the ancestral species has become extinct
What are the three basic ways to generate phylogeny?
Parsimony methods
Distance methods
Likelihood methods
For all phylogenetic methods, how is the reliability of a tree calculated?
By ‘bootstrapping’
Likelihood methods are based on a function that calculates what?
The probability that a given tree could have produced the observed data (very mathematical)
Describe how parsimony methods work
Uses the fewest number of changes needed to explain the sequences to give the best tree
Give examples of distance methods
UPGMA
Fitch-Margoliash
Neighbour joining
Distance Wagner
What is used during distance methods which makes them a lot easier to understand?
A matrix
Why is the phylogeny of genes not necessarily the phylogeny of the species?
If DNA is evolving neutrally then a pseudogene or an intron may correspond to a species tree. However, if under natural selection, e.g. Thr-Gly repeats of the period gene, then this will not necessarily give the correct species tree.
How would you start when using the UPGMA method?
Make a distance matrix of the number of amino acid or nucleotide differences and then start with the smallest difference
What does UPGMA stand for?
Unweighted pair group method of averages
Essentially, what does the maximum likelihood method involve?
Trial and error by assuming a phylogeny until a model is found that gives the best result
The maximum likelihood method is very CPU intensive and the result produced is dependent of..
The model used
Parsimony methods are complex, true or false?
False, they are simple
Parsimony methods are not biased, true or false?
True
What do parsimony methods assume?
Same characters, e.g. nucleotides are homologous and not analagous
What does the UPGMA method assume?
Same mutation rate on all branches
The neighbour-joining method assumes that there is the same mutation rate on all branches, true or false?
False
What are distance methods based on?
Step-wise progression, so sensitive to where you start the pairwise comparison
What do maximum likelihood methods depend on?
The model of evolution chosen - but tests each one so is quite robust
What bootstrap value indicates a significant result and reliable data?
Anything over 95%
How many more times frequent are transitions than transversions?
Transitions are 2-4x more
How many more possible transversions are there for a base than transitions?
2x as many transversions
Which is more ‘mutable’, asparagine or tryptophan?
Asparagine
What sort of behaviours could you analyse if wanting to construct a phylogeny of social insects?
Green parasitoidism
Orange nest building
Predation
What could you assume about the evolution of the behaviour/morphology of the fiddler crab (Uca)?
Simpler behaviour/morphology is ancestral to more complex ones
OR
Ecology determines complexity
For the fiddler crab (Uca), which species is the more ancestral, the American or the Pacific? And what does this suggest?
The American clade
So the derived Pacific species ‘lost’ morphological elements
Suggests complexity correlates with ecology not with phylogeny
What do female swordtails prefer in a male?
Males with long swords
What do female platyfish prefer in a male?
Swords
Do male swordtails have swords?
Yes
Do male platyfish have swords?
No
In the swordtail and platyfish example, female bias has caused the male to derive a character exploiting this bias, true or false?
Unknown, some phylogeny supports this idea, others clarify the sexual selection theory
Give some evidence that supports the ancient hybridisation theory of some swordtails and platyfish
In a haplotype parsimony network of mtDNA, different species do not mix mtDNA
Was there complete ancient hybridisation between the swordtails and platyfish?
Some hybridisation clearly occurred but whether some particular species evolved as hybrid species is still not clear. Maybe some evolved and then hybridised.
What type of frog calls are there?
‘Whine’
‘Chuck’
‘Squawk’
What does the phylogeny using mtDNA and nuclear gene sequence of swordtails and platyfish show?
No major split between swordtails and platyfish and suggests male swords re ancestral, not derived.
Swords lost repeatedly.
What happens when platyfish are given testosterone? What does this mean?
It gives them swords.
So swords are there, just not expressed. Suggests regulatory locus disinhibits swords in swordtails.
Explain the phylogeny that favours the sensory bias view of swordtails and platyfish
Recapitulates anatomical phylogeny.
Female preference evolved first, males exploited it because swordless outgroup females also prefer swords.
Probably due to females preferring large males - some experimental data support this view.
But phylogeny suggests swords lost in platyfish, i.e. swords are ancestral
What does a low concordance of a gene tree suggest?
Hybridisation
How is it that a species might have platyfish mtDNA but swordtail nuclear DNA?
Ancient hybridisation between female platyfish with mtDNA and male swordtail with nuclear DNA.
Then backcross of hybrid females to male swordtails so nuclear DNA predominantly derived from swordtails.
Mechanism would be hybrid female preference for swords - sexual selection
What does BUCKy stand for?
Bayesian analysis of gene trees
What method is a Bayesian tree like?
Maximum-likelihood-like but looks not for a single tree but for a larger number of trees with a high likelihood
What does BUCKy estimate?
The concordance factor of each clade
What is meant by concordance factor?
The proportion of genes that truly have the clade (bit like bootstrapping)
What does the Bayesian tree for swordtails and platyfish show?
Looks like there is significant hybridisation among species.
Partly supports the hybridisation model of some species’ evolution but you would expect a large discordance between some species if completely true.
What does the loss of ability of a fish to produce a sword mean if it is injected with testosterone?`
The fish cannot generate a sword even with the testosterone injection
(Tree consistent with sensory bias hypothesis)
Female frog ears prefer more complex frequencies than males produce. What does this suggest?
Ear tuned to other environmental feature (bias)
What type of call do some female frog species prefer even though their males only produce whines?
Prefer whines with chucks
Prefer more complex whines than males produce
What does the molecular phylogeny of frog calls support?
Sensory exploitation but two independent male events
In Ecuador, Peru and Brazil, what types of frog calls are there within an area of 20km?
Complex and simple
What does the maximum likelihood phylogeny of frog calls in Ecuador, Peru and Brazil show?
Populations are fixed for simple/complex call multiple times.
Recent divergence of populations suggesting selection not drift.
What does the microsatellite loci of frog calls from Ecuador, Peru and Brazil show?
Gene flow between nearby populations (21-28km apart) was 30x less between populations with different call types
In terms of frog calls, what do females also select for?
Local dialect of simple song
What did scientists found out about frog calls when they correlated genetic divergence of 9 microsatellite loci with geographical variables and song in 2 species in 10 populations?
Only song is significant
Consistent with sexual selection (song) driving speciation not geographical barriers
What hypothesis does the phylogenetic analysis of frog calls support?
The ‘sensory exploitation’ view of the evolution of male songs in single species
Repeated evolution of simple/complex alls within small areas, probably driven by recent selection via female choice within species
