O'Grady Lab
  • Home
  • News and Events
  • People
    • Current Members
    • Undergraduate Research
    • Past Members
  • Research
  • Publications
  • Data
    • Mitochondrial Primers
    • Nuclear Primers
    • Accession Numbers
  • Photos
  • Courses
  • Educational Outreach
  • Links

Phylogenetics and ecological niche modeling  

11/9/2012

1 Comment

 
Picture
The other day I got into a class discussion about ancestral state reconstruction, or the assignment of ancestral states based on extant taxa. Some people thought that character mapping was not scientifically sound unless you had a time machine. I, however, disagree. The utility of phylogenetics is to determine evolutionary relationships between extant taxa, and while time machines do not exist, systematists are able to make hypotheses about these relationships. I think character mapping follows the same principles and gives science more insight into diversification processes. However, one problem I do see with ancestral state reconstruction is that your analysis is only as good as your phylogenetic tree. As many people say, “junk in, junk out.” Therefore, use with caution.

One new ancestral state reconstruction method I recently learned uses the software package Phyloclim maintained by Christoph Heibl. Phyloclim is a package implemented in R that integrates species ecological niche models with phylogenetics in order to calculate and visualize niche evolution on a phylogenetic tree. To do this, the user must first create a predicted species occupancy model. This involves using ecological niche modeling software, such as Maxent, and species location data stored as a raster file--I believe this is done in a mapping program like GIS. There is a great tutorial on the Maxent website.

Patterns of niche evolution or niche conservation can then be determined by comparing the variation between niche space within and between subclades. One of two outcomes is expected: 1) either niche evolution occurs between subclades with conservation of niche space within each subclade or 2) niche conservation occurs between subclades and niche evolution occurs within each subclade. This means you could either see a divergence of niche spaces at the beginning family followed by conservation of their niche spaces or you would see niche space preserved early on in evolutionary history followed by diversification among species. Inference can then be made about ancestral niche spaces using a statistical analysis, and a statement of how climate (or other variables) may or may not result in the diversification of a group.

I really liked using this R package. The visual of ancestral state reconstruction (see figure above) is really informative and neat to look at. However, Phyloclim is still quite new and no formal tutorial from the developers exists, but there are examples in the software package complete with example data. I have yet to try using my own data in Phyloclim, but I think it’s as simple reading a .csv file of your ecological niches models and your tree file in newick or nexus format (I like this tutorial) into R. I realize this may be easier said then done, but in theory it’s simple.

Jessica Craft

Useful papers:

Evans, M. E. K., S. A. Smith, R. S. Flynn, and M. J. Donoghue. 2009. Climate, niche evolution, anddiversification of the ’bird-cage evening primroses’ (Oenothera, sections Anogra and Kleinia). Am. Nat. 173: 225-240.

Fitzpatrick, B.M & Turelli, M. 2006. The geography of mammalian speciation:mixed signals from phylogenies and range maps. Evolution 60: 601-615.

Phillips, S.J, M. Dudik, & R.E. Schapire. 2006. Maximum entropy modeling of species geographic distributions. Ecological Modeling 190: 231-259.

Warren, D., R.E. Glor, & M. Turelli. 2008. Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution. Evolution 62: 2868-2883


1 Comment
Brian Ort
11/9/2012 05:35:27 am

Niche modeling is certainly an interesting and useful tool for what we're doing. I just took a couple of workshops at the Global Information Facility (GIF) on campus to get better at it. When combined with phylogenetics, it really is a form of ancestral state reconstruction. What is most interesting to me is making predictions about future species ranges based on climate or other projections. This is really what resource managers have been trying to do for decades, and the tools are getting better. Thanks for the post.

Reply



Leave a Reply.

    Patrick

    Professor
    Cornell University

    Archives

    April 2018
    March 2018
    August 2017
    March 2017
    January 2017
    September 2015
    May 2015
    March 2015
    January 2015
    October 2014
    April 2014
    March 2014
    February 2014
    September 2013
    May 2013
    April 2013
    February 2013
    January 2013
    November 2012
    October 2012
    September 2012
    August 2012
    July 2012
    June 2012
    May 2012
    January 2012
    November 2011
    October 2011
    May 2011
    February 2011

    Categories

    All
    1090
    1091
    Alumni
    Aquatic Insects
    Arizona
    Asteia
    Barcoding
    Bennett
    Blog
    Career
    Celebrations
    Chelsea
    Climate Change
    Cornell
    Craft
    Dicranota
    Dolichopodidae
    Drosophila
    Ephydra
    Ephydridae
    Field Work
    Funding
    Goodman
    Hawaiian Drosophila
    Keys
    Kidwell
    Lapoint
    Limonia
    Magnacca
    Marrack
    Montana
    Nesophrosyne
    New Species
    Ogrady
    Ort
    Paceyn
    Pak
    Panbiogeography
    Pediciidae
    Peterson
    Phylogenetic Methods
    Publications
    Readings
    Rhaphidolabis
    Scaptomyza
    Scatella
    Schedule
    Stauffer
    Sylvain
    Talks
    Taxonomy
    Tipula
    Undergraduates
    Unicorns
    Whiteman Lab
    Wojciechowski
    Wolbachia
    Wyoming
    Yeast And Fungi

    RSS Feed