Do two genes yield the same or different phylogenetic hypotheses? Why or why not? We
may get differences in resolution if there are differences in molecular evolutionary rates
between genes, for example. Discordance between nuclear gene and mitochondrial gene trees
can also be an indicator of a history of reticulate evolution (hybridization and introgression).
This project would be a great choice for students interested in genetics, molecular
phylogenetics, and visualization.
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For this question, you would choose a taxonomic group (of modest size) and obtain genetic
data for two different markers. After determining which species have data for both genes,
you would perform a sequence alignment for each gene and build a phylogenetic tree for
each gene. If you wish, you may adapt class example scripts for some portions of the
phylogenetics analysis portion. If suitable for your data set, use a different alignment method
(such as a secondary structure model for ribosomal RNA genes) or a codon-based alignment
for protein-coding nucleotide sequences (e.g. see DECIPHER package functions). For your
phylogeny, aim to go beyond the class materials, such as through conducting model testing
(e.g. using the phangorn package) and/or maximum likelihood phylogenetic analysis. Then,
building upon that, you would examine topological congruence of the two trees through
visualization, such as using functions available through the phytools, phangorn, or
dendextend package or other resources. Y ou could also consider calculating one or more
formal metrics of phylogenetic congruence.
Tip: Choose a small data set size for this project (e.g. 10-50 species for each of two genes,
after data filtering steps).
Tips: Consider performing this project for a genus or family-level taxonomic group. Choose
genes that are supported as being helpful for resolving relationships among species within
genera or families. Examples of common genes used for phylogenetics include COI, cytb for