Spring 2019

January 28

Xie, KT, et al. 2019. DNA fragility in the parallel evolution of pelvic reduction in stickleback fish. Science 363(6422):81-84. doi:10.1126/science.aan1425

February 4 — Polygenic and Complex Traits, Pt 1

Mendes, FK, et al. 2018. A multispecies coalescent model for quantitative traits. eLife 7:e36482 doi:10.7554/eLife.36482



  • Incomplete lineage sorting cannot be ignored when studying quantitative trait evolution on macroevolutionary scales.

  • Moving forward: Estimate levels of ILS from genomic data to help correct for the expected increase in trait variance caused by ILS.

February 25 — Polygenic and Complex Traits, Pt 1

Josephs, EB, et al. 2019. Detecting adaptive differentiation in structured populations with genomic data and common gardens. GENETICS early online. doi:10.1534/genetics.118.301786



  • Detecting adaptation in structured populations requires massive amounts of data and, even then, detection is difficult.

  • Moving forward: In what parameter space are we simply out of luck? When is there too much structure or when is adaptive phenotypic divergence too weak?

Briefly noted

Gupta, K, et al. The Evolution of Placental Invasion and Cancer Metastasis are Causally Linked. BioRxiv doi:10.1101/528646

Alves, JM, et al. 2019. Parallel adaptation of rabbit populations to myxoma virus. Science doi:10.1126/science.aau7285

Glassberg, EC, et al. 2019. Evidence for Weak Selective Constraint on Human Gene Expression. GENETICS 211(2). doi:10.1534/genetics.118.301833

Dung, SK, et al. 2019. Illuminating Women’s Hidden Contribution to Historical Theoretical Population Genetics. GENETICS 211(2). doi:10.1534/genetics.118.301833

Lowry, DB, et al. 2019. Mechanisms of a locally adaptive shift in allocation among growth, reproduction, and herbivore resistance in Mimulus guttatus. Evolution. doi:10.1111/evo.13699

Harkness, A, E Goldberg, Y Brandvain. 2019. The evolutionary response of mating system to heterosis. Journal of Evolutionary Biology. doi:10.1111/jeb.13430

March 4th — The current debate on sweeps, Pt 1

Jensen, JD. 2014. On the unfounded enthusiasm for soft selective sweeps. Nature Communications 5.



  • How might the presence or prevalence of linked deleterious variation affect our expectations for the incidence of soft sweeps?

  • What is the expected pattern of haplotype variation from an incomplete sweep?

Briefly Noted

Buffalo, V, and G Coop. 2019. The Linked Selection Signature of Rapid Adaptation in Temporal Genomic Data. BioRxiv doi:10.1101/559419

Aumer, D, et al. 2019. A Single SNP Turns a Social Honey Bee (Apis mellifera) Worker into a Selfish Parasite. Molecular Biology and Evolution 36(3). doi:10.1093/molbev/msy232.

Paulose, J, J Hermisson, and O Hallatschek. 2019. Spatial soft sweeps: Patterns of adaptation in populations with long-range dispersal. PLoS Genetics doi:10.1371/journal.pgen.1007936

Dixon, JR, et al. 2018. Integrative detection and analysis of structural variation in cancer genomes. Nature Genetics 50:1388–1398

March 11 — The current debate on sweeps, Pt 2

Schrider, DR, and AD Kern. 2017. Soft Sweeps Are the Dominant Mode of Adaptation in the Human Genome. Molecular Biology and Evolution 34(8). 1863–1877. 10.1093/molbev/msx154.


RB Harris, A Sackman, JD Jensen. 2018. On the unfounded enthusiasm for soft selective sweeps II: Examining recent evidence from humans, flies, and viruses. PLoS Genetics. 10.1371/journal.pgen.1007859

Schrider, DR, and AD Kern. 2018. On the well-founded enthusiasm for soft sweeps in humans: a reply to Harris, Sackman, and Jensen. Zenodo. doi:10.5281/zenodo.1473781.

April 1 — Fitness to phenotype and genotype, pt 1

Bontrager, M, and AL Angert. 2018. Gene flow improves fitness at a range edge under climate change. Evolution Letters 3(1)



  • Gene flow can be beneficial at a range edge — “swamping” effects of gene flow on local adaptation may be nuanced

  • Gene flow from historically warmer populations may be important for long-term fitness as climate changes

  • What else do we need to know to apply this knowledge to conservation?

Briefly Noted

Week, B, and S Nuismer. 2019. The measurement of coevolution in the wild. Ecology letters 22(4)

Marcais, G, et al. 2018. MUMmer4: A fast and versatile genome alignment system. PLoS Computational Biology 14(1). e1005944. https://doi.org/10.1371/journal.pcbi.1005944

Sackman, AM, RB Harris, and JD Jensen. 2019. Inferring Demography and Selection in Organisms Characterized by Skewed Offspring Distributions. Genetics 211(3): 1019-1028

April 8 — Fitness to phenotype to genotype, pt 2

Papkou, A, et al. 2019. The genomic basis of Red Queen dynamics during rapid reciprocal host–pathogen coevolution. PNAS 116(3) 923-928



  • The underlying genomic basis to coevolutionary dynamics is likely complex even if phenotypic/fitness patterns appear consistent and predictable.

  • Possible that a combination of (in)complete sweeps and frequency dependent allele shifts could result in fluctuating fitness relationships.

  • How might dynamics change with a genetically diverse pathogen?

Briefly noted

El-Brolosy, MA, et al. 2019. Genetic compensation triggered by mutant mRNA degradation. Nature 568: 193-197

Ma, Z, et al. 2019. PTC-bearing mRNA elicits a genetic compensation response via Upf3a and COMPASS components. Nature 568: 259-263

April 15 — Fitness to phenotype to genotype, pt 3

Kooyers, NJ, et al. 2019. Lagging Adaptation to Climate Supersedes Local Adaptation to Herbivory in an Annual Monkeyflower. American Naturalist


Briefly Noted

Thompson, KA, MM Osmond, D Schluter. 2019. Parallel genetic evolution and speciation from standing variation. Evolution Letters 3(2): 129-141

Ramos, SE, and FP Schiestl. 2019. Rapid plant evolution driven by the interaction of pollination and herbivory. Science 364(6436): 193-196

Stetter, MG, K Thornton, J Ross-Ibarra. 2018. Genetic architecture and selective sweeps after polygenic adaptation to distant trait optima. PLoS Genetics 14(11). e1007794. https://doi.org/10.1371/journal.pgen.1007794

Nardou, R, et al. 2019. Oxytocin-dependent reopening of a social reward learning critical period with MDMA. Nature.