Razib Khan One-stop-shopping for all of my content

August 22, 2018

General laws of macroevolution from phylogenetics

Filed under: Macroevolution,phylogenetics — Razib Khan @ 12:10 am

I’ve been following the Evolution 2018 Meeting in Montpelier on Twitter. A lot of the stuff is interesting, though over my head. In biology, I began with a fascination with natural history. What we might term macroevolution today. I was that kid carrying out The Dinosaur Heresies when I was nine. But aside from the specific, broad patterns of diversification and extinction over geological time periods were clear. Over the years I wended my way through biochemistry, molecular evolution, and finally population genetics. My professional interests, therefore, have generally focused on patterns of variation on a microevolutionary scale. Stuff within species, not across species.

But I’m still quite interested in big picture evolutionary processes. I’m not a fan of Stephen Jay Gould, but I did read the highly repetitive and prolix The Structure of Evolutionary Theory. And, I have a decent course background in phylogenetics because of where I studied (well, at least in Bayesian and ML computational methods and the big picture theory). So I followed very closely the reports of Luke Harmon’s Presidential address at the meeting this year.

After the talk came the preprint, Macroevolutionary diversification rates show time-dependency:

For centuries, biologists have been captivated by the vast disparity in species richness between different groups of organisms. Variation in diversity is widely attributed to differences between groups in how fast they speciate or go extinct. Such macroevolutionary rates have been estimated for thousands of groups and have been correlated with an incredible variety of organismal traits. Here we analyze a large collection of phylogenetic trees and fossil time series and report a hidden generality amongst these seemingly idiosyncratic results: speciation and extinction rates follow a scaling law where both depend strongly on the age of the group in which they are measured. This time-scaling has profound implications for the interpretation of rate estimates and suggests there might be general laws governing macroevolutionary dynamics.

The primary text is pretty lucid. The major figure is at the top of the post. The authors tried to check if the pattern that they saw was a statistical artifact, and they don’t think it is. Rather, they believe that the pattern is a reflection of some genuine material or dynamic processes latent in the origin and extinction of species. They conclude that “This scenario, consistent [with] our results, would imply that the scaling of rates of sedimentation, phenotypic divergence, molecular evolution, and diversification with time all might share a common cause.” More concretely, earlier in the paper they note that the K-T boundary resulted in an extinction and speciation event (for dinosaurs and mammals respectively). But these massive catastrophic shocks don’t seem to happen regularly as much as randomly.

There’s a lot to chew on in the preprint. I can’t judge the technical details, which are in the supplements. For example, I have heard of BAMM before and know some of its general principles because of my coursework, but I’ve never done this sort of analysis extensively, and so I’ve never developed a good intuition about what passes the smell test and what doesn’t. But it strikes me that this field of phylogenetics is nevertheless very accessible to those who are non-scientists but genuinely interested in evolutionary biology. I recommend you read the preprint closely if you do aver an interest in this field.

Addendum: Note that I still think that evolution is scale independent on a deep level. Should I change my mind based on this? I don’t see why.

April 21, 2011

The Court Jester and the averaging fallacy

The Pith:Climatic and biological evolutionary pressures on an ecosystem complement at different scales. Neither is “dominant,” as that framing is not even wrong.

Yesterday I alluded to the Court Jester hypothesis of evolutionary change, which is often contrasted with the Red Queen hypothesis. The main embarrassment for me as a person who fancies himself a fan of evolutionary process is that I hadn’t ever heard of the Court Jester Hypothesis before yesterday. Therefore I went back to the paper which outlined many of the basic ideas of the model in 2001, Distinguishing the effects of the Red queen and Court Jester on Miocene mammal evolution in the northern Rocky Mountains. To be fair, the hypothesis itself is a tightening of a range of ideas which were long in the air. I did know, for example, about the Turnover-pulse hypothesis. These are all a set of models which emphasize the abiotic selective pressures on life forms, as opposed to the biotic ones. An abiotic pressure would be something like the Younger Dryas cold snap. A biotic pressure might be an exotic invasive species spreading through the ...

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