Phylogenies Flashcards
phylogeny
the history of descent of a group of organisms from a common ancestor
phylogenetic tree
comparison of traits, individuals with common traits placed together
trait
one form of a character
e.g. blue flower colour
character
a feature of an organism
e.g. flower colour
homologous traits
traits inherited from a common ancestor
derived traits
traits that differ from ancestor
homoplasies
similar character in 2 or more taxa that are not derived from a common ancestor
example of a homoplasy
wings - found in insects, mammals (bats) and birds
monophyletic taxa
include ALL descendents of common ancestor
paraphyletic taxa
include SOME, but not all, descendent of a common ancestor
polyphyletic taxa
includes members with MORE THAN ONE recent common ancestor
outgroup
a lineage closely related to the focal group
convergent evolution
independent evolution of similar traits due to similar selection pressure
parallel evolution
independent evolution of common trait in organisms sharing distant relatives
traits used in phylogenies
- morphology and developmental
- molecular
advantages of molecular traits
- directly reflect underlying process of evolution
- vast number of potential traits
- can detect difference between very closely related organisms
- not affected by the environment
- mutations random with specific probabilities, number of mutations can be used to calibrate evolutionary time (molecular clocks)
molecular clocks
mutations random with specific probabilities, number of mutations can be used to calibrate evolutionary time
disadvantages of molecular traits
- can’t get DNA from too far back
- complexity - duplicates of the same gene
transition
purine -> purine
pyrimidine -> pyrimidine
transversion
purine -> pyrimidine
pyrimidine -> purine
non-coding DNA located in…
introns
coding DNA located in…
exons
examples of non-coding DNA
repetitive sequences, pseudogenes
synonymous
DO NOT change amino acid
more commonly fixed in evolution
non-synonymous
DO change amino acid
nonsense
prematurely terminate genes
mitochondrial gene example for analysis (evolution)
cytochrome C - highly conserved gene
calibration of molecular clock
alpha-globin
What is the C-value?
the weight of the genome (in grams)
explaining the C-paradox
1 - genomes differ in the amount of repetitive DNA
2 - some species have more than 2 copies of each chromosome (polyploidy)
polyploidy
more than 2 copies of the haploid chromosome
Single or Low-Copy sequences
- genes including promoters, exons and introns
- pseudogenes
Repetitive DNA
middle-repetitive and highly-repetitive
- multiple copy genes - increased expression -> more of gene product produced
- telomeres - facilitate accurate copying of linear DNA molecule
Mobile elements
transposons and retrotransposons
transposons
mobile DNA elements that can move from one place to another
retrotransposons
can increase in copy number via the production of an RNA intermediate followed by insertion of a DNA copy into the genome
what are SSRs?
Simple sequence repeats
- short sequence - 1-5 bp
AKA micro-satellites
why is number of repeats not well copied?
slippage
________ contain large tracts of micro-satellites.
Centromeres
mutation will normally lead to loss of function
(to) pseudogenes
accumulated gene duplication leads to…
gene clusters
euploidy
containing a chromosome number that is a multiple of the haploid number
aneuploidy
extra or fewer copies of one chromosome or part of a chromosome guides
chromosomal rearrangements
inversions and translocations
