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  • Multiple sequence alignment of homologous cytochrome C protein sequences using Jalview viewer.

    Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence...

    Learning Objectives
    At the end of this lesson, students will be able to:
    • Define similarity in a non-biological and biological sense when provided with two strings of letters.
    • Quantify the similarity between two gene/protein sequences.
    • Explain how a substitution matrix is used to quantify similarity.
    • Calculate amino acid similarity scores using a scoring matrix.
    • Demonstrate how to access genomic data (e.g., from NCBI nucleotide and protein databases).
    • Demonstrate how to use bioinformatics tools to analyze genomic data (e.g., BLASTP), explain a simplified BLAST search algorithm including how similarity is used to perform a BLAST search, and how to evaluate the results of a BLAST search.
    • Create a nearest-neighbor distance matrix.
    • Create a multiple sequence alignment using a nearest-neighbor distance matrix and a phylogram based on similarity of amino acid sequences.
    • Use appropriate bioinformatics sequence alignment tools to investigate a biological question.
  • Using phylogenetics to make inferences about historical biogeographic patterns of evolution.

    Building Trees: Introducing evolutionary concepts by exploring Crassulaceae phylogeny and biogeography

    Learning Objectives
    Students will be able to:
    • Estimate phylogenetic trees using diverse data types and phylogenetic models.
    • Correctly make inferences about evolutionary history and relatedness from the tree diagrams obtained.
    • Use selected computer programs for phylogenetic analysis.
    • Use bootstrapping to assess the statistical support for a phylogeny.
    • Use phylogenetic data to construct, compare, and evaluate the role of geologic processes in shaping the historical and current geographic distributions of a group of organisms.
  • A A student assists Colorado Parks & Wildlife employees spawning greenback cutthroat trout at the Leadville National Fish Hatchery; B greenback cutthroat trout adults in a hatchery raceway; C tissue samples collected by students to be used for genetic analysis (images taken by S. Love Stowell)

    Cutthroat trout in Colorado: A case study connecting evolution and conservation

    Learning Objectives
    Students will be able to:
    • interpret figures such as maps, phylogenies, STRUCTURE plots, and networks for species delimitation
    • identify sources of uncertainty and disagreement in real data sets
    • propose research to address or remedy uncertainty
    • construct an evidence-based argument for the management of a rare taxon