Rawcopy is an R package for processing of Affymetrix CytoScan HD, CytoScan 750k and SNP 6.0 microarray raw intensities (CEL files). It uses data from a large number of reference samples to produce log ratio for total copy number analysis and B-allele frequency for allele-specific copy number and heterozygosity analysis. Rawcopy achieves higher signal-to-noise ratio than commonly used free and proprietary alternatives, leading to improved identification of copy number alterations. In addition, Rawcopy visualises each microarray sample for assessment of technical quality, patient identity and genome-wide absolute copy number states.

Sex chromosomes play a prominent role in development and evolution and have several characteristic features that distinguish them from autosomes. Across diverse taxa, recombination is typically suppressed at the sex-determining region (SDR) and proportionally elevated in the remainder of the chromosome or pseudoautosomal region (PAR). However, in most model taxa the sex chromosomes are ancient and highly differentiated from autosomes, and thus little is known about recombination dynamics of homomorphic sex chromosomes with incipient sex-determining mechanisms. Here we examine male function (pollen production) and female function (fruit production) in crosses of the dioecious octoploid strawberry Fragaria chiloensis in order to map the small and recently evolved SDR controlling both traits and to examine recombination patterns on the young ZW chromosome. The SDR occurs in a narrow 280kb window, in which the maternal recombination rate is lower than in the orthologous paternal region and the genome-wide average rate, but within the range of autosomal rate variation. In contrast to the SDR, the ZW recombination rate in the PAR is much higher than the rates of the ZZ or autosomal linkage groups, substantially overcompensating for the SDR rate. By extensively sequencing sections of the SDR vicinity in several crosses and unrelated plants, we show that W-specific divergence is elevated within a portion of the SDR and find only a single SNP to be in high linkage disequilibrium with sex, suggesting that any W-specific haplotype protected from recombination is not large. We hypothesize that selection for recombination suppression within the small SDR may be weak, but that fluctuating sex ratios could favor elevated recombination in the PAR to remove deleterious mutation on the W. Thus these results illuminate the recombination dynamics of a nascent sex chromosome with a modestly diverged SDR, which could be typical of other dioecious plants.

Due to the lack of recombination, the male-specific region of the Y chromosome (MSY) is a unique resource for tracking the genetic history of populations. The MSY is also enriched for large, nearly identical repetitive regions known as amplicons, which harbor many of the genes essential for spermatogenesis. In humans, sequence diversity on the unique segment of the MSY is greatly reduced compared to the autosomes, an observation consistent with the action of strong selection. Here, we analyze 9 chimpanzee (representing three subspecies: Pan troglodytes schweinfurthii, Pan troglodytes ellioti, and Pan troglodytes verus) and two Pan paniscus male whole-genome sequences to assess Y chromosome nucleotide and ampliconic copy-number diversity across the Pan genus. In total, we identified 23,946 Pan spp. SNVs across 4.2 million callable sites. Comparisons with autosomal, X chromosome, and mitochondrial sequences from the same samples indicate that nucleotide diversity on the chimpanzee MSY is reduced relative to neutral expectations with an equal sex ratio. Additionally, the estimated common chimpanzee Y chromosome TMRCA (0.44 mya [0.31-0.56]) is half the age of the mitochondria TMRCA (0.97 mya [0.65-1.35]), indicating an unequal sex ratio or Y chromosome selection in the common chimpanzee ancestral population. We observe that the copy-number of Y chromosome amplicons is variable amongst chimpanzees and bonobos, and identify several lineage-specific patterns, including variable copy-number of the testis-expressed genes RBMY and DAZ. We detect recurrent switchpoints of copy-number change along the ampliconic tracts across chimpanzee populations, which may be the result of localized genome instability or selective forces.

Motivation: Bioinformatics analyses have become increasingly intensive computing processes, with lowering costs and increasing numbers of samples. Each laboratory spends time creating and maintaining a set of pipelines, which may not be robust, scalable, or efficient. Further, the existence of different computing environments across institutions hinders both collabo-ration and the portability of analysis pipelines. Results: Flowr is a robust and scalable framework for designing and deploying computing pipelines in an easy-to-use fashion. It implements a scatter-gather approach using computing clusters, simplifying the concept to the use of five simple terms (in submission and dependency types). Most importantly, it is flexible, such that customizing existing pipelines is easy, and since it works across several computing environments (LSF, SGE, Torque, and SLURM), it is portable. Availability: http://docs.flowr.space

Research on the genetics of natural populations was revolutionized in the 1990′s by methods for genotyping non-invasively collected samples. However, these methods have remained largely unchanged for the past 20 years and lag far behind the genomics era. To close this gap, here we report an optimized laboratory protocol for genome-wide capture of endogenous DNA from non-invasively collected samples, coupled with a novel computational approach to reconstruct pedigree links from the resulting low-coverage data. We validated both methods using fecal samples from 62 wild baboons, including 48 from an independently constructed extended pedigree. We enriched fecal-derived DNA samples up to 40-fold for endogenous baboon DNA, and reconstructed near-perfect pedigree relationships even with extremely low-coverage sequencing. We anticipate that these methods will be broadly applicable to the many research systems for which only non-invasive samples are available. The lab protocol and software (″WHODAD″) are freely available at http://www.tung-lab.org/protocols and http://www.xzlab.org/software, respectively.

Despite the global economic and ecological importance of forest trees, the genomic basis of differential adaptation and speciation in tree species is still poorly understood. Populous tremula and P. tremuloides are two of the most widespread tree species in Northern Hemisphere. Using whole-genome re-sequencing data from 24 P. tremula and 22 P. tremuloides individuals, we find that the two species diverged ~2.2-3.1 million years ago. The approximately allopatric speciation of the two species was likely the results of the severing of the Bering land bridge combined with the onset of dramatic climatic oscillations throughout the Pleistocene. We detected moderate but also considerable heterogeneous genomic differentiation between species. Rather than being physically clustered into just a few large, discrete genomic “islands” as may be expected when species diverges in the presence of gene flow, we found that the regions of differentiation were particularly steep, narrowly defined and located in regions with substantially suppressed recombination. It appears that species-specific adaptation, mainly involving standing genetic variation via soft selective sweeps, was likely the predominant proximate cause in generating the differentiation islands between species and not local differences in permeability of gene flow. In addition, we identified multiple signatures of long-term balancing selection predating speciation in regions containing immunity and defense-related genes in both species.

The distribution of mutation fitness effects is central to evolutionary genetics. Typical univariate distributions, however, cannot model the effects of multiple mutations at the same site, so we introduce a model in which mutations at the same site have correlated fitness effects. To infer the strength of that correlation, we developed a diffusion approximation to the triallelic frequency spectrum, which we applied to data from D. melanogaster. We found a moderate correlation between the fitness effects of nonsynonymous mutations at the same codon, suggesting that both mutation identity and location are important for determining fitness effects in proteins. We validated our approach by comparing with biochemical mutational scanning experiments, finding strong quantitative agreement, even between different organisms. We also found that the correlation of mutation fitness effects was not affected by protein solvent exposure or structural disorder. Together, our results suggest that the correlation of fitness effects at the same site is a previously overlooked yet fundamental property of protein evolution.