TERM 1
What is the definition of positional homology?
DEFINITION 1
position of nucleotides in aligned homologous genes/loci
TERM 2
What are ways to obtain homologous DNA
sequences ( genes/loci)?
DEFINITION 2
sequence of a homologous gene of interest from select
taxa w/ designated primers
search database w/ a sequence of interest to find
homologues in other taxa
verify homology through alignment of sequences to
known gene of interest
TERM 3
When constructing a phylogeny with
molecular data, what are some potential
pitfalls that need to be considered?
DEFINITION 3
homoplasy in DNA evolution increases in frequency the
greater the distance between OTUs
phylogenies obtained from molecular data may reflect the
evolution of the gene & not necessarily of the OTUs
variation in rates of evolution along branches may increase the
probability of recovering the wrong tre e
the model of evolution chosen to rec onstruct the phylogeny
may be inappropriate for the sequences you have selected
TERM 4
Phylogeny reconstruction is necessarily
heuristic because...
DEFINITION 4
an exhaustive search of all possible trees is impossible for
more than a few OTUs
complex models of evolution employed to reconstruct a
phylogeny are computationally intense
tree space gets exponentially larger as the number of
OTUs increases
TERM 5
A distance corrections graph of distance
measure vs. time illustrates what principles of
molecular evolution
DEFINITION 5
distance-based phylogenetic methods that do not correct for
homoplasy may recover inaccurate evolutionary relationships
ultrametric phylogenetic methods are limited in their ability to
correct for homoplasy in distantly related OTUs
model-based phylogenetic methods that correct for the nature
of evolution have a better recover of evolutionary relationships
