BIOL 3445 Lecture Notes - Lecture 14: Molecular Phylogenetics, Phylogenetics, Base Pair
BIOL 3445.001 | Lecture #14 | 3/1/2018
Molecular Phylogenetics
OBJECTIVES
― Compare and contrast using genes to create phylogenies with using
morphological characters
― Understand that the history of genes may differ from the history of the species
carrying them
― Understand the methods used to create and analyze molecular phylogenies
― Evaluate hypotheses using molecular phylogenies
COALESCING GENES
― We can trace the “ancestry” of homologous genes back to a common ancestor
in the same way that we trace species back to a
common ancestor
― Coalescence: the geneology of any pair of
homologous alleles merges in a common ancestor
at some point in the past
o We can trace the ancestry of homologous genes back through time to a
common ancestor where they first diverged
o How do genes diverge from a common ancestor?
▪ Mutations
▪ Duplications
▪ Inversion
▪ Deletions
▪ Anything that leads to changes in existing genes that can be
passed on to offspring
― Homologous Genes (homologs): any genes related by common ancestry
o Different nucleotides or sequences at the same position in a gene
o Alternative alleles at one locus
o Orthologs: homologous genes in different species
▪ Usually have a similar function across species
▪ Homologous genes that are separated by a speciation event
▪ Evolve separately in each species
o Paralogs: genes that have been duplicated and then evolved separately
▪ Homologous genes that arise by duplication
▪ Each copy begins to evolve separately after duplication
find more resources at oneclass.com
find more resources at oneclass.com
BIOL 3445.001 | Lecture #14 | 3/1/2018
GENE TREES
― We can trace gene evolution through time just as we can trace species
evolution through time
― Gene Tree: branched lineage of homologous alleles
that traces their evolution back to an ancestral allele
o Can be completely different from species trees
― Incomplete Lineage Sorting: the evolutionary history
of the gene does not match the history of the species
carrying it
o AKA “Deep Coalescence”
― How can we use the evolutionary history of genes to get
an accurate species tree?
o Use many gene trees to get an accurate view of
history
o Consensus gene trees
o The more genes you add, the closer it will look to
the species tree
o The answer is always “add more data”
METHODS OF MOLECULAR PHYLOGENETICS
― We can use molecular data to make trees in the same way that we use
morphological data
o However, molecular data is very different, so we need to adjust our
methods
― Molecular Data Considerations:
o Only four (4) possible bases: A, G, C, T
o Thousands of “characters” can be included in a single phylogeny
o Molecular homoplasy is much more common because there are only four
possible states for each character
― Maximum Parsimony: the best tree has the fewest evolutionary steps
o Can be complicated by molecular data because not all portions of the
genome evolve in the same way
o We need to minimize homoplasy
because it will confuse our tree
o Some regions of the genome are
more likely to change than others
o Regions that experience a higher
rate of change are more likely to
include molecular homoplasies
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
Compare and contrast using genes to create phylogenies with using morphological characters. Understand that the history of genes may differ from the history of the species carrying them. Understand the methods used to create and analyze molecular phylogenies. We can trace the ancestry of homologous genes back to a common ancestor in the same way that we trace species back to a common ancestor. We can trace gene evolution through time just as we can trace species evolution through time. Gene tree: branched lineage of homologous alleles that traces their evolution back to an ancestral allele: can be completely different from species trees. Incomplete lineage sorting: the evolutionary history of the gene does not match the history of the species carrying it: aka deep coalescence . We can use molecular data to make trees in the same way that we use morphological data: however, molecular data is very different, so we need to adjust our methods.
