Evolution of dispersal kernel in laboratory populations of Drosophila melanogaster

Sudipta Tung, Abhishek Mishra, P.M. Shreenidhi, Mohammed Aamir Sadiq, Sripad Joshi, V.R. Shree Sruti, Sutirth Dey

Stress affects the epigenetic marks added by Bari-Jheh: a natural insertion associated with two adaptive phenotypes in Drosophila

Stress affects the epigenetic marks added by Bari-Jheh: a natural insertion associated with two adaptive phenotypes in Drosophila

Lain Guio, Cristina Vieira, Josefa González

Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models

Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models

Jesse Bloom

TreeToReads – a pipeline for simulating raw reads from phylogenies

TreeToReads – a pipeline for simulating raw reads from phylogenies

Emily Jane McTavish, James Pettengill, Steven Davis, Hugh Rand, Errol Strain, Marc Allard, Ruth E Timme

The Northern Arizona SNP Pipeline (NASP): accurate, flexible, and rapid identification of SNPs in WGS datasets

The Northern Arizona SNP Pipeline (NASP): accurate, flexible, and rapid identification of SNPs in WGS datasets

Jason W Sahl, Darrin Lemmer, Jason Travis, James Schupp, John Gillece, Maliha Aziz, Elizabeth Driebe, Kevin Drees, Nathan Hicks, Charles Williamson, Crystal Hepp, David Smith, Chandler Roe, David Engelthaler, David Wagner, Paul Keim

Statistics of Cellular Evolution in Leukemia: Allelic Variations in Patient Trajectories Based on Immune Repertoire Sequencing

Statistics of Cellular Evolution in Leukemia: Allelic Variations in Patient Trajectories Based on Immune Repertoire Sequencing

Hong Gao, Chunlin Wang, Junhee Seok, Marcus W Feldman, Wenzhong Xiao

A comparison of ancestral state reconstruction methods for quantitative characters

A comparison of ancestral state reconstruction methods for quantitative characters

Manuela Royer-Carenzi, Gilles Didier

Wright-Fisher construction of the two-parameter Poisson-Dirichlet diffusion

Wright-Fisher construction of the two-parameter Poisson-Dirichlet diffusion
Cristina Costantini, Pierpaolo De Blasi, Stewart N. Ethier, Matteo Ruggiero, Dario Spano

The two-parameter Poisson-Dirichlet diffusion, recently introduced by Petrov, extends the infinitely-many-neutral-alleles diffusion model, related to Kingman’s one-parameter Poisson-Dirichlet distribution and to certain Fleming-Viot processes. The additional parameter has been shown to regulate the clustering structure of the population, but is yet to be fully understood in the way it governs the reproductive process. Here we shed some light on these dynamics by formulating a K-allele Wright-Fisher model for a population of size N, involving a uniform parent-independent mutation pattern and a specific state-dependent immigration kernel. Suitably scaled, this process converges in distribution to a K-dimensional diffusion process as N→∞. Moreover, the descending order statistics of the K-dimensional diffusion converge in distribution to the two-parameter Poisson-Dirichlet diffusion as K→∞. The choice of the immigration kernel depends on a delicate balance between reinforcement and redistributive effects. The proof of convergence to the infinite-dimensional diffusion is nontrivial because the generators do not converge on a core. Our strategy for overcoming this complication is to prove \textit{a priori} that in the limit there is no “loss of mass”, i.e., that, for each limit point of the finite-dimensional diffusions (after a reordering of components by size), allele frequencies sum to one.

Rubbish DNA: The functionless fraction of the human genome
Dan Graur

Because genomes are products of natural processes rather than intelligent design, all genomes contain functional and nonfunctional parts. The fraction of the genome that has no biological function is called rubbish DNA. Rubbish DNA consists of junk DNA, i.e., the fraction of the genome on which selection does not operate, and garbage DNA, i.e., sequences that lower the fitness of the organism, but exist in the genome because purifying selection is neither omnipotent nor instantaneous. In this chapter, I (1) review the concepts of genomic function and functionlessness from an evolutionary perspective, (2) present a precise nomenclature of genomic function, (3) discuss the evidence for the existence of vast quantities of junk DNA within the human genome, (4) discuss the mutational mechanisms responsible for generating junk DNA, (5) spell out the necessary evolutionary conditions for maintaining junk DNA, (6) outline various methodologies for estimating the functional fraction within the genome, and (7) present a recent estimate for the functional fraction of our genome.

Geographic cline analysis as a tool for studying genome-wide variation: a case study of pollinator-mediated divergence in a monkeyflower

Geographic cline analysis as a tool for studying genome-wide variation: a case study of pollinator-mediated divergence in a monkeyflower

Sean Stankowski, James M. Sobel, Matthew A. Streisfeld