1. Molecular data assisted morphological analyses

2. Polysiphonia study Molecular data assisted morphological analyses
Use molecular data to define the limits of species.
“barcoding”, need some baseline information to set the molecular limits of a species
Polysiphonia study
rbcL sequences as molecular data
The level of expected intraspecific sequence divergence established by McIvor et al. (2001, Mol. Ecol. 10: ) in a study where they compared rbcL sequence data with karyological and interbreeding data.
Sequences generated from multiple North Carolina specimens
sequence similarity used for species identification
phylogenetic analyses used to determine evolutionary relationships
(an advantage of rbcL as a “barcoding” gene)
Species specimen tree based on phylogenetic tree used for character state mapping
Phylogenetic tree

3. Analyze morphological characters in each molecularly-defined specimen

4. Determine the consistency of morphological characters within species

5. Trees, Phylogenetic Analyses and other ventures down the Dark Side.

6. Phylogenetic Analyses, Trees, etc.
Tree terminology
internal node
Node: point at which 2 or more branches diverge
terminal node
or OTU
Internal node: hypothetical last common ancestor
Terminal node: molecular or morphological data from which the tree is derived
(OTUs = Operational Taxonomic Units)
Clade: a node and everything arising from it
terminal node
or OTU
internal node
clade
clade

7. Monophyletic group: a group in which all members are derived from a unique common ancestor
Polyphyletic group: a group in which all members are not derived from a unique common ancestor. The common ancestor of the group has many descendants that are not in the group
Paraphyletic group: a group that excludes some of the descendants of the common ancestor

8. A couple of points about trees… A B
All branches can rotate freely around a node
i.e. B is not more closely related to C than A, and C is not more closely related to D than E C D E
Branch lengths may be proportional to the hypothesized distance between nodes – PAUP’s “phylogram”
Branch lengths may be be drawn as equal between nodes – “cladograms”
(these are used when one is interested only in the branching pattern)
DNA or protein sequence trees are hypotheses of how a particular DNA locus or protein has evolved.
We assume that the way the DNA or protein has evolved reflects the way the species has evolved i.e. gene tree = species tree
This may or may not reflect reality.
i.e. molecules do not necessarily trump morphology, etc. (las moléculas no necesariamente morfología del triunfo)

9. DNA sequence analyses (protein as well)

10. DNA sequence analyses (protein as well)
Molecular trees are only as good as the data they are based upon
i.e. GARBAGE IN = GARBAGE OUT (Basura en = basura hacia fuera)
Sequence alignment is the most important step in phylogenetic analysis
same sites in different sequences need to be homologous
area to possibly remove because of uncertain homology between sites
inferred insertion/deletion mutations (gaps)

11. DNA sequence analyses (protein as well)
Analysis methods
Distance methods: based on similarity between OTUs
Optimization methods
Parsimony: searching for the tree that requires the least number of mutational steps
Maximum Likelihood: searching for the most likely (tree with highest probability) given the OTUs (sequences) and model of evolution
Bayesian: searching for a set of trees in which the likelihoods are so similar that changes between them are essentially random
The choice of analysis method may be deeply philosophical or it may be based on practicality
What method can I use and get a result in a reasonable amount of time?

12. DNA sequence analyses (protein as well)
Testing Trees
Decay Analysis or Bremer Support Values: a test used in parsimony analyses where one determines how many steps less parsimonious than minimal is a particular branch in your tree no longer resolved in the consensus of all possible trees that length.
Bootstrapping: a way to test the level of support in your data for a particular relationship in your tree.
by default most programs will show bootstrap values when they are greater than 50
but, does a bootstrap value of 50 mean anything?
Hillis & Bull (1993) Systematic Biology 42: (tested bootstrap values based on a known phylogeny)
Wilson’s Rule:
60-80, is there other evidence to support the relationship, be cautious
80-90, usually pretty solid
90-100, solid and unlikely to be misleading