The Time-Scale of Recombination Rate Evolution in Great Apes

Laurie S Stevison, August E Woerner, Jeffrey M Kidd, Joanna L Kelley, Krishna R Veeramah, Kimberly F McManus, Carlos D Bustamante, Michael F Hammer, Jeffrey D Wall
doi: http://dx.doi.org/10.1101/013755

We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequencing data of 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez et al. 2013). Using species-specific PRDM9 sequences to predict potential binding sites, we identified an important role for PRDM9 in predicting recombination rate variation broadly across great apes. Our results are contrary to previous research that PRDM9 is not associated with recombination in western chimpanzees (Auton et al. 2012). Additionally, we show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time-scale of complete hotspot turnover. We quantified the variation in the biased distribution of recombination rates towards recombination hotspots across great apes. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10‐15 Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, based on multiple linear regression analysis, we found that various correlates of recombination rate persist throughout primates including repeats, diversity, divergence and local effective population size (Ne). Our study is the first to analyze within- and between-species genome-wide recombination rate variation in several close relatives.

The P-element strikes again: the recent invasion of natural Drosophila simulans populations

Robert Kofler, Tom Hill, Viola Nolte, Andrea Betancourt, Christian Schlötterer
doi: http://dx.doi.org/10.1101/013722

The P-element is one of the best understood eukaryotic transposable elements. It invaded Drosophila melanogaster populations within a few decades, but was thought to be absent from close relatives, including D. simulans. Five decades after the spread in D. melanogaster, we provide evidence that the P-element has also invaded D. simulans. P-elements in D. simulans appear to have been acquired recently from D. melanogaster probably via a single horizontal transfer event. Expression data indicate that the P-element is processed in the germline of D. simulans, and genomic data show an enrichment of P-element insertions in putative origins of replication, similar to that seen in D. melanogaster. This ongoing spread of the P-element in natural populations provides an unique opportunity to understand the dynamics of transposable element spreads and the associated piRNA defense mechanisms.

Distributions of topological tree metrics between a species tree and a gene tree

Jing Xi, Jin Xie, Ruriko Yoshida
(Submitted on 10 Jan 2015)

In order to conduct a statistical analysis on a given set of phylogenetic gene trees, we often use a distance measure between two trees. In a statistical distance-based method to analyze discordance between gene trees, it is a key to decide “biological meaningful” and “statistically well-distributed” distance between trees. Thus, in this paper, we study the distributions of the three tree distance metrics: the edge difference, the path difference, and the precise K interval cospeciation distance, between two trees: first, we focus on distributions of the three tree distances between two random unrooted trees with n leaves (n≥4); and then we focus on the distributions the three tree distances between a fixed rooted species tree with n leaves and a random gene tree with n leaves generated under the coalescent process with given the species tree. We show some theoretical results as well as simulation study on these distributions.