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Reed A. Cartwright

Publications and source records attributed to Reed A. Cartwright.

2 recordsLinked to original sources

The effect of the dispersal kernel on isolation-by-distance in a continuous population

Under models of isolation-by-distance, population structure is determined by the probability of identity-by-descent between pairs of genes according to the geographic distance between them. Well established analytical results indicate that the relationship between geographical and genetic distance depends mostly on the neighborhood size of the population, $N_b = 4πσ^2 D_e$, which represents a standardized measure of dispersal. To test this prediction, we model local dispersal of haploid individuals on a two-dimensional torus using four dispersal kernels: Rayleigh, exponential, half-normal and triangular. When neighborhood size is held constant, the distributions produce similar patterns of isolation-by-distance, confirming predictions. Considering this, we propose that the triangular distribution is the appropriate null distribution for isolation-by-distance studies. Under the triangular distribution, dispersal is uniform within an area of $4πσ^2$ (i.e. the neighborhood area), which suggests that the common description of neighborhood size as a measure of a local panmictic population is valid for popular families of dispersal distributions. We further show how to draw from the triangular distribution efficiently and argue that it should be utilized in other studies in which computational efficiency is important

q-bio.PE

A Composite Genome Approach to Identify Phylogenetically Informative Data from Next-Generation Sequencing

We have developed a novel method to rapidly obtain homologous genomic data for phylogenetics directly from next-generation sequencing reads without the use of a reference genome. This software, called SISRS, avoids the time consuming steps of de novo whole genome assembly, genome-genome alignment, and annotation. For simulations SISRS is able to identify large numbers of loci containing variable sites with phylogenetic signal. For genomic data from apes, SISRS identified thousands of variable sites, from which we produced an accurate phylogeny. Finally, we used SISRS to identify phylogenetic markers that we used to estimate the phylogeny of placental mammals. We recovered phylogenies from multiple datasets that were consistent with previous conflicting estimates of the relationships among mammals. SISRS is open source and freely available at https://github.com/rachelss/SISRS.

q-bio.PE