Seminar Computational Biology 2018-19

recent theoretical, experimental, and phylogenetic
advances related to topics discussed in the course.

Get an overview of the papers and
choose one topic for presentation and one topic for discussion.

NOTE: be critical: inclusion does not mean ‘good’

1  Prebiotic evolution

Moderate sex between protocells can balance between a decrease in assortment load and an increase in parasite spread

Z Vig-Milkovics, I Zachar, Á Kun, A Szilágyi… - Journal of theoretical …, 2019 - Elsevier

Coupled catabolism and anabolism in autocatalytic RNA sets

S Arsène, S Ameta, N Lehman, AD Griffiths… - Nucleic acids …, 2018 - academic.oup.com

Molecular trade-offs in RNA ligases affected the modular emergence of complex ribozymes at the origin of life

N Dhar, MS Weinberg… - Royal Society …, 2017 - rsos.royalsocietypublishing.org

2  Fitness landscapes

Experimental Determination and Prediction of the Fitness Effects of Random Point Mutations in the Biosynthetic Enzyme HisA
Erik Lundin; Po-Cheng Tang; Lionel Guy; Joakim Näsvall; Dan I Andersson

Molecular Biology and Evolution, Volume 35, Issue 3, 1 March 2018, Pages 704–718, https://doi.org/10.1093/molbev/msx325

On the deformability of an empirical fitness landscape by microbial evolution

D Bajić, JCC Vila, ZD Blount, A Sanchez - bioRxiv, 2018 - biorxiv.org

Evolution on the biophysical fitness landscape of an RNA virus

A Rotem, AWR Serohijos, CB Chang… - … and evolution, 2018 - academic.oup.com

Multi-environment fitness landscapes of a tRNA gene

C Li, J Zhang - Nature ecology & evolution, 2018 - nature.com

3 Evolution of mutation rates 

Mutator genomes decay, despite sustained fitness gains, in a long-term experiment with bacteria

Alejandro Couce, Larissa Viraphong Caudwell, Christoph Feinauer, Thomas Hindré, Jean-Paul Feugeas, Martin Weigt, Richard E. Lenski, Dominique Schneider and Olivier Tenaillon   https://doi.org/10.1073/pnas.1705887114


Sign of selection on mutation rate modifiers depends on population size

Yevgeniy Raynes, C. Scott Wylie, Paul D. Sniegowski and Daniel M. WeinreichPNAS March 27, 2018. 115 (13) 3422-3427; published ahead of print March 12, 2018. https://doi.org/10.1073/pnas.1715996115

Adaptive tuning of mutation rates allows fast response to lethal stress in Escherichia coliT Swings, B Van den Bergh, S Wuyts,

E Oeyen… - Elife, 2017 - cdn.elifesciences.org


4 Evolvability

Adding levels of complexity enhances robustness and evolvability in a multilevel genotype–phenotype map

P Catalán, A Wagner… - Journal of The …, 2018 - rsif.royalsocietypublishing.org

Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

A Rajeh, J Lv, Z Lin - BMC genomics, 2018 - bmcgenomics.biomedcentral.com

Evolutionary potential of transcription factors for gene regulatory rewiring

C Igler, M Lagator, G Tkačik, JP Bollback… - Nature ecology & …, 2018 - nature.com


5 Evolvability:  repeated rapid changes

Random sequences rapidly evolve into de novo promoters

AH Yona, EJ Alm, J Gore - Nature communications, 2018 - nature.com

Frequent ploidy changes in growing yeast cultures

Y Harari, Y Ram, M Kupiec - Current genetics, 2018 - Springer

Repeated cis-regulatory tuning of a metabolic bottleneck gene during evolution

MC Kuang, J Kominek, WG Alexander… - Molecular biology …, 2018 - academic.oup.com

6 Eco-evolutionary dynamics and diversity

Emergence of evolutionary stable communities through eco-evolutionary tunneling

SE Kotil, K Vetsigian - bioRxiv, 2018 - biorxiv.org

Strain-level diversity drives alternative community types in millimetre-scale granular biofilms.

Leventhal GE, Boix C, Kuechler U, Enke TN, Sliwerska E, Holliger C, Cordero OX.

Nat Microbiol. 2018 Sep 24. doi: 10.1038/s41564-018-0242-3. [Epub ahead of print]

Assembly of microbial communities in replicate nutrient‐cycling model ecosystems follows divergent trajectories, leading to  alternate stable states
E Pagaling, K Vassileva, CG Mills… - Environmental …, 2017 - Wiley Online Library



7 Pattern formation and selection pressures

Emergence of evolutionary driving forces in pattern-forming microbial populations

J Kayser, CF Schreck, QQ Yu… - … Transactions of the …, 2018 - royalsocietypublishing.org

Limited role of spatial self-structuring in emergent trade-offs during pathogen evolution

V Buendía, MA Muñoz, S Manrubia - arXiv preprint arXiv:1804.08463, 2018 - arxiv.org


Multigenerational memory and adaptive adhesion in early bacterial biofilm communities

CK Lee, J de Anda, AE Baker… - Proceedings of the …, 2018 - National Acad Sciences

Stability of host-parasite systems: you must differ to coevolve

FS Berezovksaya, GP Karev, MI Katsnelson, YI Wolf… - bioRxiv, 2018 - biorxiv.org




8  Evolution of multicellularity

Trait heritability in major transitions

MD Herron, SA Zamani-Dahaj… - BMC biology, 2018 - bmcbiol.biomedcentral.com

Synergistic cooperation promotes multicellular performance and unicellular free-rider persistence
WW Driscoll, M Travisano - Nature communications, 2017 - nature.com


9  Coupling of intracellular, cellular and multicellular process (CPM models)

Mesoscopic energy minimization drives Pseudomonas aeruginosa biofilm morphologies and consequent stratification of antibiotic activity based on cell metabolism

MV Sheraton, KH Yam, CH Tan, HS Oh… - Antimicrobial agents …, 2018 - Am Soc Microbiol

Differential tissue growth and cell adhesion alone drive early tooth morphogenesis: An ex vivo and in silico study

M Marin-Riera, J Moustakas-Verho… - PLoS computational …, 2018 - journals.plos.org

 Virtual cardiac monolayers for electrical wave propagation

N Kudryashova, V Tsvelaya, K Agladze, A Panfilov - Scientific Reports, 2017 - nature.com