Free Artificial Life (XIV edition) and Other Evolution Readings

Here is some Artificial Life for your summer reading. The Proceedings of Artificial Life XIV (complement to the conference at the end of this month in New York City) is a peer-reviewed venue for papers covering the following topics: evolutionary dynamics, soft robots, agent behavior, collective behaviors, social dynamics and evolution, and cellular automata/ self-organizing systems.

And continuing in the spirit of evolutionary scholarship, here are a few more readings from the queue in the last few months. I would call it the "summer of evolution", but every summer is the season of evolution.

I. Reticulating Clades (not Splines) and the Three Domains

Is it possible that the three domains of life are not monophyletic? A new study in Nature Reviews Microbiology [1] using cutting-edge phylogenetic methods suggests that they are not [2]. As an alternative, they suggest the ring of life hypothesis summarized above, with reticulations between each domain's clade Perhaps we are all not just Eukaryotic, and in a manner that does not directly involve symbiosis.

II. Saturday Morning Skepticism

Saturday Morning Breakfast Cereal meets potential evolutionary mechanisms. This comic from Zach Weinersmith is a joke about Horizonal Gene Transfer (HGT). Which got me to thinking: how over-hyped is HGT? The following article [3] and blog posts [4, 5] should give you some idea, as well as to the true scope of the phenomenon. Short answer: selective in Prokaryotes, nearly non-existent in Eukaryotes, and the enabler of salterns, sushi, worms and aphids [3, 6].

NOTES:

[1] McInerney, J.O., O’Connell, M.J., and Pisani, D.   The hybrid nature of the Eukaryota and a consilient view of life on Earth. Nature Reviews Microbiology, doi:10.1038/nrmicro3271 (2014).

[2] McInerney, J.   The three domains of life hypothesis has been falsified. Bioinformatics and Molecular Evolution Unit blog (2014).

[3] Zhaxybayeva, O. and Doolittle, W.F.   Lateral Gene Transfer. Current Biology, 21(7), R242-R246 (2011).

[4] Coyne, J.   How important is lateral Gene Transfer? Why Evolution is True blog, April 13 (2011).

[5] Kuchner, T.   Horizontal Gene Transfer Takes a Turn: Expansins from Plants to their Bacterial and Eukaryotic Parasites. Molecular Evolution Forum blog, March 14 (2014).

[6] Boto, L.   Horizontal gene transfer in the acquisition of novel traits by metazoans. Proceedings of the Royal Society B, 281, 20132450 (2014).

The diverse places where HGT occurs. COURTESY: Figure 1 in [3].