Visualizing niche conservatism

In the context of Vanessa Marcelino’s Msc thesis on the evolutionary dynamics of Halimeda seaweeds we were trying to visualize niche conservatism or the lack thereof across a whole bunch of species simultaneously.

As it turns out, making a heat map of niche model similarities gave a very satisfactory result. We calculated two niche overlap measures (Schoener’s D and Warren’s I) for the species’ Maxent models using ENM Tools. The resulting matrices were merged into one with Schoener’s D in the top right triangle and Warren’s I in the lower left triangle. Species were sorted in the matrix in the order that they appeared in the phylogeny, so related species are closer together in the matrix. The similarity values were then converted to colors along a green-yellow-red color gradient with MatrixGradients. The result looks like this (follow this link for PDF version):

heat map

Looks very cool. Well, mostly red and hot actually… The first striking pattern is that D values are on average lower than I values. The fact that almost the entire figure is red indicates that niches are highly conserved in Halimeda. There is also a green-yellowish cross going across the figure (as a horizontal and a vertical band of dissimilar niches). This band represents the species that have invaded colder water and these are related to one another, so they lie together in the matrix. The first column/row is also very dissimilar to all the rest. This is the sole Mediterranean species, which occurs in much colder water than all other species in the genus.

Here are the legend and the way the table was built, just to complete the picture:


  1. How about presenting the niche similarities by incorporating the phylogenetic structure of the species? You could order the species according to their phylogenetic relatedness (~ somewhat similar to heatmaps of gene families to visualise expression data).

    • heroen said:

      Hi Oli, that’s actually what we did here. The order of the species in the rows/columns corresponds to their order of appearance in a ladderized rooted phylogram. So closely related species are, on average, closer to each other in the rows/columns, the inevitable exception being when adjoining rows/columns represent species from different deeply branching clades. It would have been informative to add the phylogeny on the plot to show the species’ relatedness.

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