Applications of Phylogenetic Reconstruction Flashcards
what are sources of systematic error?
sequence data/ multiple sequence alignment
residues included in analysis that aren’t related by susbstitutions
what are counter measures?
carefully examine multiple sequence alignments - remove regions that are likely to be misaligned
compare results of different algorithms or run algorithms with different starting conditions
what are bootstrapping values?
the proportion of agreement of trees that were inferred from bootstrapping
what is Bayesian posterior probabilities?
MCMC a stimulation algorithm - moves from one tree to another and in long run look at tree in proportion to their posterior probabilities e.g darwins finches
why are phylogenetics important in conservation?
prioritises organims for inclusion in conservation programmes - takes into account - costs, probability of extinction and phylogenetic diversity
how is the domain system supported?
by data from many sequenced genomes
what is polytomy?
when a relationship cannot be fully resolved due to dichotomies
what does the tree of life tell us about the domains?
that archae and eukaryotes are more closely related to each other than bacteria - there have been interchanges of genes between organisms in different domains
what is horizontal gene transfer?
movement of genes from one genome to another by exchange of transposable elements and plasmids
why is horizontal gene transfer useful?
explains disparaties between gene trees
key in evolution of pro/eukaryotes
can we combine different phylogenetic estimates across the tree of life?
summaries can capture conflict/consensus
conflict handled by ranking input phylogenies - a higher ranking branch will be included in supertree preferentially to a branch of lower input
taxonomy always ranked last - so can’t overrule input phylogenies
