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  1. haplotypes
    the alternative dna sequence of a gene
  2. polymorphic
    when a species carries two or more haplotypes of a given gene
  3. gene tree
    phylogeneic tree showing evolutionary relationships among haplotypes
  4. unrooted tree
    phylogenetic tree without a root, showing more similar species closer to each other than to more different species, no nodes
  5. scoring character
    homplasy is common and there could be several trees
  6. adaptive radiation
    can occur relatively fast without leaving enough evolutionary time for intermediate ancestors to aquire distinct synapomorphies, makes node difficult
  7. gene phylogenies
    may not agree with species phylogenies because of incomplete lineage sorting
  8. hybridization
    between closely related species may obscure their true phylogenetic relationship which may result in a reticulated (netlike) tree
  9. horizontal gene transfer
    possibly mediated by viruses that transfer a few genes of one species into the genome of another species
  10. polytomy
    A speciation event is defined as the dichotomous branching of one ancestor species into two new species (a dichotomy). When a phylogeny is not resolved entirely, it may contain unresolved nodes with three of more new species radiating from one ancestor (sometimes referred to as a “star phylogeny”. Such a star phylogeny may suggest a very “rapid” burst of speciation, at the scale of geological time.
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