Construction of Gene and Species Trees from Sequence Data incl. Orthologs, Paralogs, and Xenologs

Construction of Gene and Species Trees from Sequence Data incl. Orthologs, Paralogs, and Xenologs
Marc Hellmuth, Nicolas Wieseke

Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged after a speciation) is crucial and lies at the heart of many genomic studies. However, existing methods that rely only on 1:1 orthologs to infer species trees are strongly restricted to a small set of allowed genes that provide information about the species tree. The use of larger gene sets that consist in addition of non-orthologous genes (e.g. so-called paralogous or xenologous genes) considerably increases the information about the evolutionary history of the respective species. In this work, we introduce a novel method to compute species phylogenies based on sequence data including orthologs, paralogs or even xenologs.

Exploring the coevolution of predator and prey morphology and behavior

Exploring the coevolution of predator and prey morphology and behavior
Randal S. Olson, Arend Hintze, Fred C. Dyer, Jason H. Moore, Christoph Adami

A common idiom in biology education states, “Eyes in the front, the animal hunts. Eyes on the side, the animal hides.” In this paper, we explore one possible explanation for why predators tend to have forward-facing, high-acuity visual systems. We do so using an agent-based computational model of evolution, where predators and prey interact and adapt their behavior and morphology to one another over successive generations of evolution. In this model, we observe a coevolutionary cycle between prey swarming behavior and the predator’s visual system, where the predator and prey continually adapt their visual system and behavior, respectively, over evolutionary time in reaction to one another due to the well-known “predator confusion effect.” Furthermore, we provide evidence that the predator visual system is what drives this coevolutionary cycle, and suggest that the cycle could be closed if the predator evolves a hybrid visual system capable of narrow, high-acuity vision for tracking prey as well as broad, coarse vision for prey discovery. Thus, the conflicting demands imposed on a predator’s visual system by the predator confusion effect could have led to the evolution of complex eyes in many predators.

Flies as Ship Captains? Digital Evolution Unravels Selective Pressures to Avoid Collision in Drosophila

Flies as Ship Captains? Digital Evolution Unravels Selective Pressures to Avoid Collision in Drosophila
Ali Tehrani-Saleh, Christoph Adami

Flies that walk in a covered planar arena on straight paths avoid colliding with each other, but which of the two flies stops is not random. High-throughput video observations, coupled with dedicated experiments with controlled robot flies have revealed that flies utilize the type of optic flow on their retina as a determinant of who should stop, a strategy also used by ship captains to determine which of two ships on a collision course should throw engines in reverse. We use digital evolution to test whether this strategy evolves when collision avoidance is the sole penalty. We find that the strategy does indeed evolve in a narrow range of cost/benefit ratios, for experiments in which the “regressive motion” cue is error free. We speculate that these stringent conditions may not be sufficient to evolve the strategy in real flies, pointing perhaps to auxiliary costs and benefits not modeled in our study

A stochastic model for speciation by mating preferences

A stochastic model for speciation by mating preferences
Camille Coron, Manon Costa, Hélène Leman, Charline Smadi

Mechanisms leading to speciation are a major focus in evolutionary biology. In this paper, we present and study a stochastic model of population where individuals, with type a or A, are equivalent from ecological, demographical and spatial points of view, and differ only by their mating preference: two individuals with the same genotype have a higher probability to produce a viable offspring. The population is subdivided in several patches and individuals may migrate between them. We show that mating preferences by themselves, even if they are very small, are enough to entail reproductive isolation between patches, and consequently speciation, and we provide the time needed for this isolation to occur. Our results rely on a fine study of the stochastic process and of its deterministic limit in large population, which is given by a system of coupled nonlinear differential equations. Besides, we propose several generalisations of our model, and prove that our findings are robust for those generalisations.

The molecular chaperone DnaK accelerates protein evolution

The molecular chaperone DnaK accelerates protein evolution

Jose Aguilar-Rodriguez, Beatriz Sabater-Munoz, Victor Berlanga, David Alvarez-Ponce, Andreas Wagner, Mario A. Fares

Explaining Missing Heritability Using Gaussian Process Regression

Explaining Missing Heritability Using Gaussian Process Regression

Kevin Sharp, Wim Wiegerinck, Alejandro Arias-Vasquez, Barbara Franke, Jonathan Marchini, Cornelis A Albers, Hilbert J Kappen

Experimental evolution of modern Escherichia coli harboring an ancient Elongation Factor gene

Experimental evolution of modern Escherichia coli harboring an ancient Elongation Factor gene

Betul Kacar, Lily I Tran, Xueliang Ge, Suparna Sanyal, Eric A. Gaucher

Analytical results for directional and quadratic selection gradients for log-linear models of fitness functions

Analytical results for directional and quadratic selection gradients for log-linear models of fitness functions

Michael Morrissey, Ian B. J. Goudie

Genome-culture coevolution promotes rapid divergence in the killer whale

Genome-culture coevolution promotes rapid divergence in the killer whale

Andrew Foote, Nagarjun Vijay, Maria Avila-Arcos, Robin Baird, John Durban, Phillip Morin, Matteo Fumagalli, Richard Gibbs, Bradley Hanson, Thorfinn Korneliussen, Michael Martin, Kelly Robertson, Vitor Sousa, Filipe Vieira, Tomas Vinar, Paul Wade, Kim Worley, Laurent Excoffier, Thomas Gilbert, Jochen Wolf

BuddySuite: Command-line toolkits for manipulating sequences, alignments, and phylogenetic trees

BuddySuite: Command-line toolkits for manipulating sequences, alignments, and phylogenetic trees

Stephen R Bond, Karl E Keat, Andreas D Baxevanis