SEMINAR2020-2021

Seminar Computational Biology 2020-2021

recent computational, experimental and phylogenetic results

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

1. PREBIOTIC EVOLUTION

Emergence and diversification of a host-parasite RNA ecosystem through Darwinian evolution

T Furubayashi, K Ueda, Y Bansho, D Motooka… - Elife, 2020 - elifesciences.org

In vitro selections with RNAs of variable length converge on a robust catalytic core

M Popović, AQ Ellingson, TP Chu, C Wei… - Nucleic Acids …, 2020 - academic.oup.com

Turbulent coherent structures and early life below the Kolmogorov scale

MS Krieger, S Sinai, MA Nowak - Nature Communications, 2020 - nature.com

2. INDIVIDUAL BASED MODELS OF ECO-ECOLUTIONARY STRATEGIES.

Complex eco-evolutionary dynamics induced by the coevolution of predator-prey movement strategies

C Netz, H Hildenbrandt, FJ Weissing - bioRxiv, 2020 - biorxiv.org

Behavioral Strategy Chases Promote the Evolution of Prey Intelligence^*

AP Wagner, L Zaman, I Dworkin, C Ofria - Evolution in Action: Past …, 2020 - Springer PDF

Damage Repair versus Aging in an Individual-Based Model of Biofilms

RJ Wright, RJ Clegg, TLR Coker, JU Kreft - Msystems, 2020 - Am Soc Microbiol

3. FITNESS LANDSCAPES AND EVOLVABLITY

The Impact of Neutral Mutations on Genome Evolvability

O Tenaillon, I Matic - Current Biology, 2020 - Elsevier

Selection enhances protein evolvability by increasing mutational robustness and foldability

J Zheng, N Guo, A Wagner - Science, 2020 - science.sciencemag.org

G Genotype networks of 80 quantitative Arabidopsis thaliana phenotypes reveal phenotypic evolvability despite pervasive epistasis

G Schweizer, A Wagner - BioRxiv, 2020 - biorxiv.org

4. MUTATION RATE AND GENOME ORGANIZATION

Adapting the engine to the fuel: mutator populations can reduce the mutational load by reorganizing their genome structure

JP Rutten, P Hogeweg, G Beslon - BMC evolutionary biology, 2019 - Springer

Low mutational load and high mutation rate variation in gut commensal bacteria

RS Ramiro, P Durão, C Bank, I Gordo - PLoS biology, 2020 - journals.plos.org

Genome expansion in early eukaryotes drove the transition from lateral gene transfer to meiotic sex

M Colnaghi, N Lane, A Pomiankowski - bioRxiv, 2020 - biorxiv.org

Moderate amounts of epistasis are not evolutionarily stable in small populations

DK Sydykova, T LaBar, C Adami, CO Wilke - Journal of molecular …, 2020 -

5. DUPDELS AND ADAPTABILITY

Gene amplification as a form of population-level gene expression regulation

I Tomanek, R Grah, M Lagator… - Nature ecology & …, 2020 - nature.com

Modeling multipartite virus evolution: the genome formula facilitates rapid adaptation to heterogeneous environments^†

MP Zwart, SF Elena - Virus Evolution, 2020 - academic.oup.com

Integron activity accelerates the evolution of antibiotic resistance

C Souque, JA Escudero, C MacLean - bioRxiv, 2020 - biorxiv.org

6. MICROBIAL ECO-EVOLUTIONARY DYNAMICS AND (UN)PREDICTABILITY

Divergent Evolution of Mutation Rates and Biases in the Long-Term Evolution Experiment with Escherichia coli

Genome Biology and Evolution, Volume 12, Issue 9, September 2020, Pages 1591–1603, https://doi.org/10.1093/gbe/evaa178

Subtle Environmental Differences have Cascading Effects on the Ecology and Evolution of a Model Microbial Community^*

JR Meyer, RE Lenski - Evolution in Action: Past, Present and Future, 2020 - Springer PDF

The genetic law of the minimum

By Martin F. Polz, Otto X. Cordero Science06 Nov 2020 : 655-656

Resource conservation manifests in the genetic code

By Liat Shenhav, David Zeev Science06 Nov 2020 : 683-687

7. MULTILEVEL EVOLUTION

Nutrient status shapes selfish mitochondrial genome dynamics across different levels of selection

BL Gitschlag, AT Tate, MR Patel - Elife, 2020 - elifesciences.or

Evolutionary Biology

Adaptive evolution of nontransitive fitness in yeast

Sean W Buskirk, Alecia B Rokes, Gregory I Lang

PDF

Eco-evolutionary dynamics of nested Darwinian populations and the emergence of community-level heredity

G Doulcier, A Lambert, S De Monte, PB Rainey - Elife, 2020 - elifesciences.org

8. EVOLUTION OF MULTICELLULARITY

Emergence of diverse life cycles and life histories at the origin of multicellularity

M Staps, J van Gestel, CE Tarnita - Nature ecology & evolution, 2019 - nature.com

Division of labor and growth during electrical cooperation in multicellular cable bacteria

NMJ Geerlings, C Karman, S Trashin… - Proceedings of the …, 2020 - National Acad Sciences

De novo origins of multicellularity in response to predation

MD Herron, JM Borin, JC Boswell, J Walker… - Scientific reports, 2019 - nature.com

9. INTRACELLULAR SPATIAL ORGANIZATION

Proofreading through spatial gradients

Vahe Galstyan, Kabir Husain ... Rob Phillips

An in-silico human cell model reveals the influence of spatial organization on RNA splicing

Z Ghaemi, JR Peterson, M Gruebele… - PLoS computational …, 2020 - journals.plos.org

10. MORPHOGENESIS

Neural crest streaming as an emergent property of tissue interactions during morphogenesis

A Szabó, E Theveneau, M Turan… - PLoS computational …, 2019 - journals.plos.org

Modeling of Wnt-mediated tissue patterning in vertebrate embryogenesis

J Rosenbauer, C Zhang, B Mattes… - PLOS Computational …, 2020 - journals.plos.org