Molecular 14-17 Flashcards
What is homoplasy ?
A characteristic shared by a set of species that is not present in their common ancestor.
What is autopomorphy ?
A derived trait that is unique to a taxon
What is symplesiomorphy ?
An ancestral characteristic shared by 2 or more taxa but also shared with other taxa earlier in the clade
What is an apomorphy and what can they be used as ?
A novel evolutionary characteristic that is unique to species and all its descendants. They can be used as a defining characteristic.
What is a synapomorphy ?
a characteristic present in an ancestral species and shared exclusively by its evolutionary descendants. Forms a clade
What is a monophyletic group and give an example ?
A group that includes all the taxa derived from the most recent common ancestor
Birds and crocodiles
What is a paraphyletic group and give an example ?
A convenience taxon that does not contain all the descendants of the MRCA
reptiles
What are the 2 distance based tree methods ?
Unweighted pair group method with arithmetic means
Neighbour join tree methods
What are the 3 tree searching methods ?
Maximum parsimony
Maximum likelihood
Baysian method
How does the unweighted pair group method with arithmetic means work ?And what is a limitation ?
Simply takes the most similar taxa and draws a tree with d/2 branch then adds the next most similar taxa
Based on false assumptions
How does the neighbour joining tree work ? And what is an advantage and a disadvantage ?
Finds the shortest overall tree for each pair of taxa
Masks true uncertainty in tree branching patten
Generates single tree
How does the maximum parsimony tree work ? And what is an advantage and a disadvantage ?
Based on character states
Finds the tree topology that requires smallest number of evolutionary steps (Advantage)
May produce multiple trees of equal likelihood
How does the maximum likelihood tree work ? And what is an advantage and a disadvantage ?
Identifies the most likely tree from all possible trees in which observed sequences would occur
Only produces one tree
Computationally intensive
What are the advantages and disadvantages of the baysian method ?
Most accurate
Branch lengths can be compared
Computationally intensive
Requires MrBayes software
What can we tell from an unrooted tree ?
The level of divergence between any OTUs but cannot tell the direction of descent
How can you root a tree ?
- Outgroup rooting: Include an outgroup that diverged earlier than the ingroup (must have external evidence for divergence and not to genetically different 20/66% rule)
- Midpoint rooting- Assumes equal rates of evolution and that the longest pathway between UTOs represents the most distant separation
What is the difference between a scaled and an unscaled tree ?
Cladogram=shows clades only= unscaled
Phylogram = shows clades and levels of divergence=scaled
What happens if clades are unresolved ?
polytomy (multiple branching) resulting in confusion about common ancestors
What are the units of a scaled tree ?
(Base (pair)) substitutions per site
What does a bootstrap value assess ?
Reliability of internal nodes in a phylogenetic tree
How do you collapse a tree ?
By deleting branches with a bootstrap value of less than 50 thus causing polytomies
What is reticulate evolution ?
Network like evolution that cannot be modelled by a bifurcating tree.
What are the 8 processes support reticulate evolution
Recombination Hybridisation Polyploidy - Multiplication of chromosomes Introgression Genome fusion - Conjugation of cells Endosymbiosis HGT Incomplete lineage sorting
What is introgression ?
Back-crossing of a hybrid with one of the parental species leading to some genes being fixed in the parental .
What is an example of introgression ?
Used to explain the evolution of modern humans
What is an example (not real life) of reticulate evolution ?
An OTU arising from a recombination of 2 species that have arose from a common ancestor
What is incomplete lineage sorting ?
occurs when polymorphisms persist between speciation
events, so that the actual (true) genealogical relationship of a gene or genome region differs from the true
species branching pattern.
What is an example of incomplete lineage sorting ?
around 15% of human genes are more closely related to homologs in gorillas than to those in our true sister lineage, the chimpanzees
Why might a paper publish more than one type of phylogenetic tree for nuclear genomes and mitochondrial genomes?
mt genome much smaller so can afford to do a more intensive method such as bayesian method.
What hypothesis explains introgression ?
Stable core- Phylogenetic tree with network analysis on top
What are the 4 types of gene duplication ?
Partial gene duplication- Part of gene duplicated
Gene duplication- whole gene duplicated
Segmental duplication- 2 genes duplicated
Polysomy- Whole chromosome duplicated
What are the 2 mechanisms of gene duplication and what do they result in ?
Homologous unequal crossing over due to high sequence similarity
Non-homologous crossing over due to short sequences having some similarity
Both result in 2 chromosomal products and one is longer than before and one is shorter
What is retention rate ?
The rate at which pseudogenes become evolutionary lost
What are the 4 possibilities after gene duplication ?
Non-functionalisation- one gene loses function and is erased from genome
Conservation- Both are preserved with same function
Sub
Sub-functionalisation- Both retained with a slight function change
Neo-functionalisation- One gene has a completely new function
How can adapted conflict be resolved ?
By reversal to unifunctionality by the loss of new function
Or by gene duplication followed by subfunctionalisation
What is adapted conflict ?
When a gene acquires a new function making it bifunctional but the two functions can not be expressed together due to the phentypic effects they have on each other
What is concerted evolution ?
This is when evolution is not normal due to high numbers of repetitions in the sequence causing unequal crossing over between 2 sister chromatids in mitosis and homologous chromosomes in meiosis
What does repeated cycles of unequal crossing over cause and gene conversion ?
Causes duplicated sequences on each chromosome to become more homogenised
What is concerted evolution in terms of gene conversion ?
When evolution is not normal due to a non reciprocal recombination process in which 2 sequences interact in such away that one is converted by the other
What factors effect concerted evolution ?
More repeats = slower rate as takes longer to become homogenised
Clustered repeats= high rates
Selection
The evolution of …….. is not clock like but is effected by concerted evolution.
duplicated sequences
What is an example of unequal crossing over ?
Colour blindness
What is polyploidisation and what are the 2 types ?
Addition of a whole genome
Autopolyploidy- Doubling of genome
Allopolyploidy= Combination of 2 genome sets from different species (interbreeding)
What are the consequences of polyploidy ?
Some species no show effects in phenotype
Ofter get large cell volumes
Unstable genomes
What is aneuploidy ?
Number of chromosomes is not exact multiple of haploid set
What is genome minturisation ?
Selective use and disuse of organs could cause an organism to lose or gain traits
What limits the size of bacterial genomes ?
Constrained by selection due to limitations on bacterial cell volume and the fact that most bacterial chromosomes have one origin of replication
What are the major forces that effect genome size ?
Deletion bias
genetic drift
Why are intracellular symbionts and parasites susceptible to genome miniturisation ?
By being sequestered in hosts, These organisms no longer have to use their own genes for many functions. Those they don´t use will tend to be lost due to selection not being strong enough causing genes to be lost either by large deletions or inactivated by deleterious mutations and subsequently eroded by small deletions.
In the prokaryotic genome what is genome minturisation facilitated by ?
Specialization
What is the minimal genome ?
The genes essential for life
What are the 2 ways to synthesise a minimal genome ?
Bottom up approach: a continuous increase in molecular complexity can transform an inanimate into a self reproducing entity
Top down approach: A full genome is gradually subtracted of DNA as long as the cells retain viability
What are minimal genome factories used for ?
To produce primary gene products such as RNAs and proteins
What are the 3 approaches to estimating gene content in the minimal genome ?
The comparative genome approach
Probabilistic reconstruction of gene content in LUCA
The experimental gene activation approach
What is the problem with the comparative genome approach ?
Did not list mechanisms for the production of nucleotides and amino acids
What is the problem with Probabilistic reconstruction of gene content in LUCA approach ?
Not a single contemporary genome has been found to contain all of the ancestral gene families.
What are the problems with The experimental gene activation approach ?
Gene essentiality is environment dependent
Some genes are individual dispensable but not simultaneously
What explains GC content in most prokaryotes ?
Mutation bias
What is an important factor in determing the GC content of prokaryotes with very High and very low GC content
Selection
What is a replichore ?
A piece of dsDNA in which one strand is replicated in its entirety as leading strand and the other as lagging strand.
What is strand dependent mutation and what does it cause ?
This is when there is a difference in replication of the leading and lagging strand thus causing GC skew
What is a chirochore ?
A ssDNA with a constant positive/ negative GC/AT skew.
When is a chirochore considered a replichore ?
When replication is asymmetric
What does the existence of local skews on one strand indicate ?
Proportions of complementary nucleotides between the 2 strands deviates from racemic proportions
What are the 3 extrachromosomal elements ?
Plasmids- Autonomous replication
Cryptic plasmid- A plasmid with no described function
Episomes- Autonomous replication
What are the 3 hypothesise that explain accessory chromosomes ?
Plasmid hypothesis- Accessory chromosome evolved from a plasmid through acquiring essential genes from primary chromosome
Schism hypothesis -Evolved from split of primary chromosome into 2 unequal sizes
Lateral gene transfer - Was captured from a bacterium
What are the advantages of having accessory chromosomes ?
Replication of 2 small chromosomes is faster than the sum of the 2
Multiple chromosomes is useful due to chromosome specific gene regulation
What are the 2 theories for the evolution of the genetic code ?
The amino acid codon interaction theory: The specific codon assignments originated from chemical interactions between nucleic acid and amino acids
Frozen accident theory: the genetic code evolved to a certain point and when genomes grew the rules of translation could not be altered without effecting many proteins at once
