Recent reading: 21 Jan 2022

Rose Main Reading Room, New York Public Library (Flickr: saebaryo)

The period between semesters is supposed to be quiet. I’ve been mentally dumping things to do into this one — paper revisions, reviewing service, analysis of long-awaited new data, a first draft of a new grant, writing my (eek) application for tenure — since at least October. But SARS-CoV-2 had other plans.

I spent the first week after campus reopened in the New Year watching the number of COVID exposure alerts sent to faculty mount up until the number of buildings on campus with a reported case was greater on the first workday after the break than the peak we hit during fall Finals Week, when students flocked back for in-person exams. Pretty soon after that we got word (via the University’s Twitter and then an all-campus email sent with no prior alert to faculty) that the first three weeks of Spring 2022 would be “primarily remote instruction” … but maybe not all of it? And so in between all the other stuff I’ve been trying to figure out how to teach a botany lab from my home office. It’ll be fine, I am telling myself.

In the midst of all that, here’s what I’ve read recently:

Yeaman S. 2022. Evolution of polygenic traits under global vs local selection. Genetics doi: 10.1093/genetics/iyab134

  • One effect of natural selection acting on a polygenic trait is to shape the genetic architecture of the trait — how loci contributing to the trait are distributed across the genome, and the range of effect sizes for new mutations that rise to higher frequency under selection.
  • Selection that acts across a species whole range (global adaptation) probably has different effects than selection operating in only part of the range (local adaptation) because the latter is shaped by the interplay of selection and migration from the rest of the range.
  • Locally adapted polygenic traits should have architecture characterized by (1) fewer loci of larger effect, (2) in closer linkage disequilibrium.
  • The difference between local and global adaptation will be clearest at intermediate migration rates. As I read it: at high migration rates, global selection swamps local, and at low migration, populations experiencing different selection regimes are evolving independently enough to be, effectively, separate “global” scenarios.

Grey Monroe J, et al. 2022. Mutation bias reflects natural selection in Arabidopsis thalianaNature doi: 10.1038/s41586-021-04269-6

  • Understanding the fate of mutations is complicated by the fact that many mutations are removed from natural populations by selection before they can be observed. The authors try to identify de novomutations prior to selection in Arabidopsis, using mutation accumulation lines in which the only mutations selected against should have been those creating total inviability or sterility (which would prevent propagation of the MALs).
  • Higher GC content and expression were associated with reduced mutation probability; methylation and accessible chromatin were associated with greater mutation probability.
  • Mutation rates were indeed lower within genes after accounting for epigenomic/genome accessibility effects.
  • Genes with conserved function (“essential genes”) were more common among genes with the lowest mutation rates expected based on epigenomic effects.
  • Authors conclude this is evidence for adaptive mutation bias against deleterious mutation: “… genes subject to stronger purifying selection are maintained in epigenomic states that underlie a significant reduction in their mutation rate.” Lead author elaborates here.
  • There’s been a lot of discussion as to whether this means mutations are not “random” and that seems plainly not to be the case; it shows mutation probabilities differ across the genome, and that those differences in probabilities may reflect adaptation, but not that mutations are occurring as a causal function of their ultimate fitness effect.

Pauli B, et al. 2022. Obligate mutualistic cooperation limits evolvability. Nature Communications doi: 10.1038/s41467-021-27630-9

  • Experimental evolution comparing antibiotic resistance adaptation by E. coli strains in monoculture, or in a co-cultured mutualism based on amino acid exchange. (Monocultures were supplemented with the necessary amino acids.)
  • Mutually dependent strains either went extinct or adapted but maintained reduced population density under antibiotic concentrations to which mono-cultured (supplemented) strains could adapt.
  • The authors observed loss of mutualism as a response to the antibiotic treatment — possibly because “escaping” the mutual dependence was necessary to adapt.

Fricke EC et al. 2022. The effects of defaunation on plants’ capacity to track climate change. Science doi: 10.1126/science.abk3510

  • Built trait-based (trait matching) models to predict the seed dispersal capacity of fleshy fruited plants given available mammal and bird dispersers — traits being disperser body mass, disperser seed movement, and germination success after disperser handling, synthesized from multiple source databases
  • Validates predictions using data on novel seed dispersal interactions by introduced disperser species (nice)
  • Interpolated a global estimate of long-distance seed dispersal capacity from spatial data on disperser species community composition, and estimated how this has changed as a result of human activity driving species extinctions and introductions
  • Compared local dispersal capacities to local “climate change velocity” to assess how human activity has affected plants’ ability to disperse and track changing climates, and estimates that human activity has reduced global average climate-tracking dispersal capacity by almost 60%

Cui D-F et al. 2022. A Jurassic flower bud from China. Geoligcal Society, London, Special Publications doi: 10.1144/SP521-2021-122

What it says on the tin: fossil evidence that angiosperms date to the Jurassic, consistent with estimates based on time-calibrated phylogenies estimated from molecular data. The authors present analysis of the specimen, named Florigerminis jurassica, identifying floral buds with distinguishable tepals and the mesocarp and endocarp of an enclosed ovary.

About Jeremy Yoder

Jeremy B. Yoder is an Associate Professor of Biology at California State University Northridge, studying the evolution and coevolution of interacting species, especially mutualists. He is a collaborator with the Joshua Tree Genome Project and the Queer in STEM study of LGBTQ experiences in scientific careers. He has written for the website of Scientific American, the LA Review of Books, the Chronicle of Higher Education, The Awl, and Slate.
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