Species Data: Use and Re-use in Systematics, Evolution and Ecology

Online Resources

(short URL for this page: https://is.gd/webbKU)

Syllabus

• Course syllabus [PDF]

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Lecture 2: Tools

Please install:

• R (from CRAN, https://cran.r-project.org/)
• R-studio (https://www.rstudio.com/)

And a text editor:

• Notepad++ (for Windows; https://notepad-plus-plus.org/)
• BBEdit (For Mac; https://www.barebones.com/products/bbedit/)

For this lecture, here are the files (Right-click, Save As...):

• R script: lecture2.R
• Example data: mydata.txt

Before tomorrow, please install the following R packages:

  taxize, ape, phangorn, seqinr, rentrez,
  maps, mapdata, raster, maptools, dismo,
  vegan, picante

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Lecture 3: Species Names

• R script (right-click, Save As...): lecture3+4.R

Lecture outline:

• The nature of species
• The practice of taxonomy
• Working with Names
  • R exercise: taxize
• Taxon Concepts
  • Taxon Concept Mapping
• The problem with names
• Alternatives to traditional taxonomy
  • “e-Taxonomy”
  • From classes to distance
• Sharing taxonomic data

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Lecture 4: Traits

Lecture outline:

• Why species differ
• Encoding traits
  • Individuals vs. Species
    • R exercise: variation
  • Photographs
• Species identification
  • Borneo tree key
  • R exercise: identification
• Sharing data
  • “Big Data”
  • R Exercise: downloading DNA data

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Lecture 5: Phylogenies

• R script (right-click, Save As...): lecture5+6.R

Lecture outline:

• Phylogenies
  • Exercise: Working with phylogenies in R
• Phylogenetic reconstruction
  • Methods
  • Phylogenetic reconstruction in R
  • CIPRES
• Traits on trees
  • Exercise: ACE in R
• Re-using trees

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Lecture 6: Biogeography

Lecture outline:

• Spatial data
  • Map making in R
  • (For your own time: GIS analysis in R data)
• Occ. plus environmental: Species distribution modeling
  • See http://rspatial.org/sdm/
• Occ. plus phylogeny: Historical Biogeography
  • BioGeoBEARS example data

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Lecture 7: Ecology

• R script (right-click, Save As...): lecture7.R

Lecture outline:

• Autecology
• Community Ecology
  • R: vegan
  • R: EcoSimR
• Phylogenetic community ecology
  • Exercise: picante

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Lecture 8: Sharing biodiversity data

Lecture outline:

• Sharing data
  • Why share data?
  • Psychology
• Standards
• Where to get data?
  • Names: Namebanks (ITIS, CoL, ThePlantList, uBio, GNA)
  • Integrated names, phylogenies, literature: Bionames
  • Genes: Genbank, DDBJ, BoLD
  • Occurrences (Collections): GBIF
  • Phylogenies: TreeBase, oToL, Phylomatic
  • Specimen photos: iDigBio, Jstor Plants, Morphbank
  • Characters/Traits: Morphobank
  • Documents: BHL, (Scihub!)
  • Field Photos: iNaturalist
• How to share data?
  • Exercise: Darwin Core Archives
  • Exercise: iNaturalist
• Closing

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References

• Some references I used during the course can be found here.

Glossary

EDIT ME!