Cristian Tomasetti, Bert Vogelstein
(Submitted on 21 Jan 2015)
This manuscript has been written to address questions related to our recent publication (Science 347:78-81, 2015). We appreciate the many reactions to this paper that have been communicated to us, either privately or publicly. The following addresses several of the most important statistical and technical issues related to our analysis and conclusions. Our responses to non-technical questions are available at this http URL
Mutation detection in candidate genes for parauberculosis resistance in sheep
Bianca Moioli, Luigi De Grossi, Roberto Steri, Silvia D’Andrea, Fabio Pilla
doi: http://dx.doi.org/10.1101/014035
The marker-assisted selection exploits anonymous genetic markers that have been associated with measurable differences on complex traits; because it is based on the Linkage Disequilibrium between the polymorphic markers and the polymorphisms which code for the trait, its success is limited to the population in which the association has been assessed. The identification of the gene with effect on the target and the detection of the functional mutations will allow selection in independent populations, while encouraging studies on gene expression. The results of a genome-wide scan performed with the Illumina Ovine SNP50K Beadchip, on 100 sheep, 50 of which positive at paratuberculosis serological assessment, identified two candidate genes of immunity response, the PCP4 and the CD109, located in proximity of the markers with different allele frequency in positive and negative sheep. The coding region of the two genes was directly sequenced: three missense mutations were detected: two in the PCP4 gene and one in the second exon of the CD109 gene. The PCP4 mutations had a very low frequency (.12 and .07) so making hazardous to hypothesize their direct effect on immune response. On the contrary, the mutation detected in the CD109 gene showed a strong linkage disequilibrium with the anonymous marker. Direct sequencing of the DNA of sheep of different populations showed that disequilibrium was maintained. Allele frequency at the hypothesized marker associated to immune response, calculated for other breeds of sheep, showed that the marker allele potentially associated to disease resistance is more frequent in the local breeds and in breeds that have not been submitted to selection programs.
Yan Huang, Deniz Erezyilmaz
doi: http://dx.doi.org/10.1101/014027
Many phytophagous insect species are ecologic specialists that have adapted to utilize a single host plant. Drosophila sechellia is a specialist that utilizes the ripe fruit of Morinda citrifolia, which is toxic to its sibling species, D. simulans. Here we apply multiplexed shotgun genotyping and QTL analysis to examine the genetic basis of resistance to M. citrifolia fruit toxin in interspecific hybrids. We find that at least four dominant and four recessive loci interact additively to confer resistance to the M. citrifolia fruit toxin. These QTL include a dominant locus of large effect on the third chromosome (QTL-IIIsima) that was not detected in previous analyses. The small-effect loci that we identify overlap with regions that were identified in selection experiments with D. simulans on octanoic acid and in QTL analyses of adult resistance to octanoic acid. Our high-resolution analysis sheds new light upon the complexity of M. citrifolia resistance, and suggests that partial resistance to lower levels of M. citrifolia toxin could be passed through introgression from D. sechellia to D. simulans in nature. The identification of a locus of major effect, QTL-IIIsima, is an important step towards identifying the molecular basis of host plant specialization by D. sechellia.
Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs
Courtney L Kagan, Nicholas E Banovich, Bryan J Pavlovic, Kristen Patterson, Irene Gallego Romero, Jonathan K Pritchard, Yoav Gilad
doi: http://dx.doi.org/10.1101/013888
The advent of induced pluripotent stem cells (iPSCs) revolutionized Human Genetics by allowing us to generate pluripotent cells from easily accessible somatic tissues. This technology can have immense implications for regenerative medicine, but iPSCs also represent a paradigm shift in the study of complex human phenotypes, including gene regulation and disease. Yet, an unresolved caveat of the iPSC model system is the extent to which reprogrammed iPSCs retain residual phenotypes from their precursor somatic cells. To directly address this issue, we used an effective study design to compare regulatory phenotypes between iPSCs derived from two types of commonly used somatic precursor cells. We show that the cell type of origin only minimally affects gene expression levels and DNA methylation in iPSCs. Instead, genetic variation is the main driver of regulatory differences between iPSCs of different donors.
Rates of karyotypic evolution in Estrildid finches differ between island and continental clades
Daniel M Hooper, Trevor D Price
doi: http://dx.doi.org/10.1101/013987
Reasons why chromosomal rearrangements spread to fixation and frequently distinguish related taxa remain poorly understood. We used cytological descriptions of karyotype to identify large pericentric inversions between species of Estrildid finches (family Estrildidae) and a time-dated phylogeny to assess the genomic, geographic, and phylogenetic context of karyotype evolution in this group. Inversions between finch species fixed at an average rate of one every 2.26 My. Inversions were twice as likely to fix on the sex chromosomes compared to the autosomes, possibly a result of their repeat density, and inversion fixation rate for all chromosomes scales with range size. Alternative mutagenic input explanations are not supported, as the number of inversions on a chromosome does not correlate with its length or map size. Inversions have fixed 3.3× faster in three continental clades than in two island chain clades, and fixation rate correlates with both range size and the number of sympatric species pairs. These results point to adaptation as the dominant mechanism driving fixation and suggest a role for gene flow in karyotype divergence. A review shows that the rapid karyotype evolution observed in the Estrildid finches appears to be more general across birds, and by implication other understudied taxa.
MultiMeta: an R package for meta-analysing multi-phenotype genome-wide association studies
Dragana Vuckovic, Paolo Gasparini, Nicole Soranzo, Valentina Iotchkova
doi: http://dx.doi.org/10.1101/013920
Summary: As new methods for multivariate analysis of Genome Wide Association Studies (GWAS) become available, it is important to be able to combine results from different cohorts in a meta-analysis. The R package MultiMeta provides an implementation of the inverse-variance based method for meta-analysis, generalized to an n-dimensional setting. Availability: The R package MultiMeta can be downloaded from CRAN Contact: dragana.vuckovic@burlo.trieste.it
RNA-guided gene drives can efficiently bias inheritance in wild yeast
James E DiCarlo, Alejandro Chavez, Sven L Dietz, Kevin M Esvelt, George M Church
doi: http://dx.doi.org/10.1101/013896
Inheritance-biasing elements known as “gene drives” may be capable of spreading genomic alterations made in laboratory organisms through wild populations. We previously considered the potential for RNA-guided gene drives based on the versatile CRISPR/Cas9 genome editing system to serve as a general method of altering populations. Here we report molecularly contained gene drive constructs in the yeast Saccharomyces cerevisiae that are typically copied at rates above 99% when mated to wild yeast. We successfully targeted both non-essential and essential genes and showed that the inheritance of an unrelated “cargo” gene could be biased by an adjacent drive. Our results demonstrate that RNA-guided gene drives are capable of efficiently biasing inheritance when mated to wild-type organisms over successive generations.
Digit evolution in gymnophthalmid lizards
Juliana Roscito, Pedro M. S. Nunes, Miguel T Rodrigues
doi: http://dx.doi.org/10.1101/013953
Background The tetrapod limb is a highly diverse structure, and reduction of the limbs accounts for much of the phenotypes observed within species. Squamate reptiles represent one of the many lineages in which the limbs have been greatly modified from the pentadactyl generalized pattern; within the group, limb-reduced morphologies can vary from minor reductions in size of elements to complete limblessness, with several intermediate forms in between. Even though limb reduction is widespread, it is not clear what are the evolutionary and developmental mechanisms involved in the formation of reduced limb morphologies. Methods In this study, we present an overview of limb morphology within the microteiid lizard group Gymnophthalmidae, focusing on digit number. Results We show that there are two major groups of limb-reduced gymnophthalmids. The first group is formed by lizard-like – and frequently pentadactyl – species, in which minor reductions (such as the loss of 1-2 phalanges mainly in digits I and V) are the rule; these morphologies generally correspond to those seen in other squamates. The second group is formed by species showing more drastic losses, which can include the absence of an externally distinct limb in adults. We also show the expression patterns of Sonic Hedgehog (Shh) in the greatly reduced fore and hindlimb of a serpentiform gymnophthalmid. Conclusions Our discussion focus on identifying shared patterns of limb reduction among tetrapods, and explaining these patterns and the morphological variation within the gymnophthalmids based on the current knowledge of the molecular signaling pathways that coordinate limb development.
Dissecting phylogenetic signal and accounting for bias in whole-genome data sets: a case study of the Metazoa
Marek L Borowiec, Ernest K Lee, Joanna C Chiu, David C Plachetzki
doi: http://dx.doi.org/10.1101/013946
Transcriptome-enabled phylogenetic analyses have dramatically improved our understanding of metazoan phylogeny in recent years, although several important questions remain. The branching order near the base of the tree is one such outstanding issue. To address this question we assemble a novel data set comprised of 1,080 orthologous loci derived from 36 publicly available genomes and dissect the phylogenetic signal present in each individual partition. The size of this data set allows for a closer look at the potential biases and sources of non-phylogenetic signal. We assessed a range of measures for each data partition including information content, saturation, rate of evolution, long-branch score, and taxon occupancy and explored how each of these characteristics impacts phylogeny estimation. We then used these data to prepare a reduced set of partitions that fit an optimal set of criteria and are amenable to the most appropriate and computationally intensive analyses using site-heterogeneous models of sequence evolution. We also employed several strategies to examine the potential for long-branch attraction to bias our inferences. All of our analyses support Ctenophora as the sister lineage to other Metazoa, although support for this relationship varies among analyses. We find no support for the traditional view uniting the ctenophores and Cnidaria (jellies, anemones, corals, and kin). We also examine phylogenetic placement of myriapods (centipedes and millipedes) and find it more sensitive to the type of analysis and data used. Our study provides a workflow for minimizing systematic bias in whole genome-based phylogenetic analyses.
Ecological patterns of genome size variation in salamanders
Bianca Sclavi, John Herrick
Comments: 19 Pages, 4 figures, 1 supplementary figure
Subjects: Genomics (q-bio.GN); Populations and Evolution (q-bio.PE)
Salamanders (urodela) have among the largest vertebrate genomes, ranging in size from 10 to over 80 pg. The urodela are divided into ten extant families each with a characteristic range in genome size. Although changes in genome size often occur randomly and in the absence of selection pressure, non-random patterns of genome size variation are evident among specific vertebrate lineages. Here we report that genome size in salamander families varies inversely with species richness and other ecological factors: clades that began radiating earlier (older crown age) tend to have smaller genomes, higher levels of diversity and larger geographical ranges. These observations support the hypothesis that urodel families with larger genomes either have a lower propensity to diversify or are more vulnerable to extinction than families with smaller genomes.
Haldane's Sieve 