Lyons et al looked at many community data sets from the last 300 million years and tested for pairs of species that are more aggregated (co-occur) or segregated than expected by chance. They found that in modern data sets, there are more segregated than aggregated species pairs, and the opposite pattern in fossil data sets, with a breakpoint about 6000 years ago, suggesting a severe impact from early agriculture. This was a surprising finding, especially given the presence-absence data used by the authors.
We argue that Lyons et al result is a product of
- poor data set selection (some of which were addressed by a corrigendum)
- artefacts in the breakpoint analysis
- data-set size related artefacts in the identification of segregated and aggregated species pairs
Together, these problems mean that the results of Lyons et al cannot be substantiated.
Lyons and co-authors, predictable, disagree with our conclusion.
Once I get back to Bergen from Makerere, I plan to write something about the reply, and some of our findings that we didn’t have space for in our comment.