Reading, Thinking About Diatoms
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Andy laid out a possible division for the two chapters in our meeting yesterday, when I pushed him to do so (being completely stuck myself as to where that division should fall). He grouped the description of the morphospace, the loadings, what the axes mean, comparison to NMDS, comparison to the phylogeny, and correlation with genetic distance into one paper, then the disparity and diversity measures through time and various subsampling approaches into another. He suggested using the stacked space-through-time plot as the culmination of the first paper, though I’m now wondering whether it wouldn’t make more sense to use that in the second paper, if the theme of the first is morphospace and phylogeny and the theme of the second is morphospace and diversity or morphospace through time. I think it is gong to be key to figure out exactly what the theme of each paper is. I don’t know right now, that’s for sure.
In any case, before next week I will need to finish up the last plots and analysis, which includes picking a few characters or groups of characters relevant to biological hyptotheses about what might be going on in the morphospace through time. In order to approach this, I need to read, so that’s what’s on the docket for today. Read about diatom evolution, and take notes about what sorts of characters I might use to test the ideas that are out there.
A couple of thoughts that occur regarding what the real diversity/morphospace history might be: we know that the range-through diversity and morphospace history provides a true minimum estimate. Everything we observe we know was there—the difficulty is knowing how much more there was. From that perspective, of course, it’s silly to subsample anything, since we are throwing out data to generate curves with less diversity and fewer observations when we already know that in reality there was more. But, since we don’t know how much more, we subsample and standardize in order to compare like and like to see relative changes. We never want to read anything into the axis labels on a subsampled curve. So what the subsampled morphospace curve tells us is that we have to consider the possibility that sampling bias is part of what generates the picture we see when we look at the raw or ranged-through pattern. It doesn’t say that the true picture is the subsampled picture.
Perhaps one of the things we can look at is disparity and diversity per site? Like we have alpha and beta diversity, can we have alpha and beta disparity?
Another thought—can the biomarker record help us here at all? If preservation really is the enemy, and there were are lot more diatoms around and we’re just not capturing them due to our poor sampling, perhaps we can see supporting evidence from molecular fossils? The Sinninghe-Damste paper on C25-HBI biomarkers for rhizosolenoid diatoms suggests they were around, and abundant, by about 90 mya. How does that compare with the occurrences of rhizosolenia taxa in the Neptune database?
