Fractality and Entropic Scaling in the Chromosomal Distribution of Conserved Noncoding Elements in the Human Genome

Fractality and Entropic Scaling in the Chromosomal Distribution of Conserved Noncoding Elements in the Human Genome

Dimitris Polychronopoulos, Labrini Athanasopoulou, Yannis Almirantis

On the causes of evolutionary transition:transversion bias

On the causes of evolutionary transition:transversion bias

Arlin Stoltzfus, Ryan W. Norris

Evolution of complex phenotypes through successions of adaptive steps

Evolution of complex phenotypes through successions of adaptive steps
Tin Y. Pang, Martin Lercher

The emergence of complex phenotype is a fascinating question of evolutionary biology, and we sought to understand preadaptation which facilitated the development of complex phenotypes, in the context of bacterial metabolic network. Genes coordinated for a phenotype are likely to cluster on the same place of the genome, which so allows horizontal gene transfer (HGT) to pass the phenotype to another bacterium. But for a complex phenotype, its genes are clustered on different places of the genome cannot be transferred adaptively; it is preadaptation, which refers to adaptive transfer of a segment relevant to a complex phenotype for other purposes, that allows it later to be recruited for the complex phenotype. To search for preadaptation in the evolutionary history of E. coli, we reconstructed the ancestral genomes from various strains, identified the transferred genes, grouped them into possible transferred segments, and analyzed the gains in nutritional phenotypes corresponding to the acquisitions of segments of metabolic genes. Properties of these HGT segments inferred from data are enumerated and compared with a model of HGT, which shows that: 1) HGT segments are likely to adaptive, and segments carrying reactions essential to phenotypic gains but non-adaptive are rare; 2) the landscape of segment transfer for complex phenotypes is directional and path-dependent; 3) cooperation between HGT segments to support various nutritional phenotypes are observed to be more frequent than expected, which serves as an evidence to preadaptation in the evolution of bacterial metabolic network.

Wolbachia infection in a sex-structured mosquito population carrying West Nile virus

Wolbachia infection in a sex-structured mosquito population carrying West Nile virus
József Z. Farkas, Stephen A. Gourley, Rongsong Liu, Abdul-Aziz Yakubu

Wolbachia is possibly the most studied reproductive parasite of arthropod species. It appears to be a promising candidate for biocontrol of some mosquito borne diseases. We begin by developing a sex-structured model for a Wolbachia infected mosquito population. Our model incorporates the key effects of Wolbachia infection including cytoplasmic incompatibility and male killing. We also allow the possibility of reduced reproductive output, incomplete maternal transmission, and different mortality rates for uninfected/infected male/female individuals. We study the existence and local stability of equilibria, including the biologically relevant and interesting boundary equilibria. For some biologically relevant parameter regimes there may be multiple coexistence steady states including, very importantly, a coexistence steady state in which Wolbachia infected individuals dominate. We also extend the model to incorporate West Nile virus (WNv) dynamics, using an SEI modelling approach. Recent evidence suggests that a particular strain of Wolbachia infection significantly reduces WNv replication in Aedes aegypti. We model this via increased time spent in the WNv-exposed compartment for Wolbachia infected female mosquitoes. A basic reproduction number R0 is computed for the WNv infection. Our results suggest that, if the mosquito population consists mainly of Wolbachia infected individuals, WNv eradication is likely if WNv replication in Wolbachia infected individuals is sufficiently reduced.

Algorithmic Methods to Infer the Evolutionary Trajectories in Cancer Progression

Algorithmic Methods to Infer the Evolutionary Trajectories in Cancer Progression
Giulio Caravagna, Alex Graudenzi, Daniele Ramazzotti, Rebeca Sanz-Pamplona, Luca De Sano, Giancarlo Mauri, Victor Moreno, Marco Antoniotti, Bud Mishra

The evolutionary nature of cancer relates directly to a renewed focus on the voluminous NGS (next generation sequencing) data, aiming at the identification of explanatory models of how the (epi)genomic events are choreographed in cancer initiation and development. However, despite the increasing availability of multiple additional -omics data, this quest has been frustrated by various theoretical and technical hurdles, mostly related to the dramatic heterogeneity and temporality of the disease. In this paper, we build on our recent works on selectivity relation among driver mutations in cancer progression and investigate their applicability to the modeling problem – both at the population and individual levels. On one hand, we devise an optimal, versatile and modular pipeline to extract ensemble-level progression models from cross-sectional sequenced cancer genomes. The pipeline combines state-of-the-art techniques for sample stratification, driver selection, identification of fitness-equivalent exclusive alterations and progression model inference. We demonstrate this pipeline’s ability to reproduce much of the current knowledge on colorectal cancer progression, as well as to suggest novel experimentally verifiable hypotheses. On the other hand, we prove that our framework can be applied, mutatis mutandis, in reconstructing the evolutionary history of cancer clones in single patients, as illustrated by an example with multiple biopsy data from clear cell renal carcinomas.

Handicap hypothesis implies emergence of dimorphic mating displays

Handicap hypothesis implies emergence of dimorphic mating displays
Sara M. Clifton, Rosemary I. Braun, Daniel M. Abrams

Since 1975 Zahavi’s handicap principle has provided an elegant explanation for extravagant ornaments in the animal world: namely, that ornaments advertise fitness and must be costly in order to enforce honest signaling. Here, we show that populations of animals subject to the handicap principle may be forced to split into distinct subgroups of differing ornament size. We verify our claims via simple mathematical analysis and real-world data, including a composite data set of ornament size distributions from many distinct species, all of which are consistent with model predictions.

MTG2: An efficient algorithm for multivariate linear mixed model analysis based on genomic information

MTG2: An efficient algorithm for multivariate linear mixed model analysis based on genomic information

Sang Hong Lee, Julius van der Werf

Genomic variant calling: Flexible tools and a diagnostic data set

Genomic variant calling: Flexible tools and a diagnostic data set

Michael Lawrence, Melanie A Huntley, Eric Stawiski, Art Owen, Thomas D Wu, Leonard D Goldstein, Yi Cao, Jeremiah Degenhardt, Jason Young, Joseph Guillory, Sherry Heldens, Marlena Jackson, Somasekar Seshagiri, Robert Gentleman

Deep sequencing of environmental DNA isolated from the Cuyahoga River highlights the utility of river water samples to query surrounding aquatic and terrestrial biodiversity

Deep sequencing of environmental DNA isolated from the Cuyahoga River highlights the utility of river water samples to query surrounding aquatic and terrestrial biodiversity

Matthew Cannon, James Hester, Amanda Shalkhauser, Ernest R Chan, Kyle Logue, Scott T Small, David Serre

Complete assembly of novel environmental bacterial genomes by MinIONTM sequencing

Complete assembly of novel environmental bacterial genomes by MinIONTM sequencing

Daniel J Turner, Xiaoguang Dai, Simon Mayes, Sissel Juul