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2014 GENETICS Web Spotlight


2013 Web Spotlight


 

Since 1916, GENETICS has sought to publish significant advances in the field. To be accepted for publication, manuscripts must provide new insights into a biological process or demonstrate novel and creative approaches to an important biological problem or describe development of new resources, methods, technologies, or tools. And the study must be of interest to a wide range of genetics and genomics investigators. The editors of GENETICS seek to attract and publish articles that they believe will have a high impact on the field.

 

While it has a long and illustrious history, GENETICS has changed: it is not your mentor's journal. The editors make decisions quickly – in around 32 days – without sacrificing the excellence and scholarship for which the journal has long been known. GENETICS is constantly innovating; some of the new and expanded types of content include:

  • YeastBook – a comprehensive compendium of reviews that presents the current state of knowledge of the molecular biology, cellular biology, and genetics of the yeast Saccharomyces cerevisiae.

  • Educational Primers – tied to a current article in GENETICS, these educational resources lay out the necessary background (i.e., what was the question and why did that question matter?), explain the hypothesis or approach, describe the methodology, guide the reader through the results, and provide a precise summation of the discussion.

  • Genetic Toolbox Reviews – describes practical and intellectual resources available for the study of less commonly used experimental organisms.

  • Reviews

Thompson Reuters JCR Impact Factor (2014): 5.963
EigenFactor (2014): 0.06335
Cited Half-life (2014): >10 years

 

View the Editorial Board  |  Read GENETICS  Submit your manuscript  |  Contact us

 


 

 What's Inside the Current Issue of GENETICS

 

Monday, June 6 2016 09:44:53 AM

ISSUE HIGHLIGHTS [Issue Highlights]


Monday, June 6 2016 09:44:53 AM

Joshua Lederberg on Bacterial Recombination [Classic]

Johnston, M.



Monday, June 6 2016 09:44:53 AM

Curt Stern on Somatic Crossing Over [Classic]

Birchler, J. A.



Monday, June 6 2016 09:44:53 AM

Massively Parallel Genetics [Commentary]

Shendure, J., Fields, S.


Human genetics has historically depended on the identification of individuals whose natural genetic variation underlies an observable trait or disease risk. Here we argue that new technologies now augment this historical approach by allowing the use of massively parallel assays in model systems to measure the functional effects of genetic variation in many human genes. These studies will help establish the disease risk of both observed and potential genetic variants and to overcome the problem of "variants of uncertain significance."



Monday, June 6 2016 09:44:53 AM

A Brief History of Schizosaccharomyces pombe Research: A Perspective Over the Past 70 Years [Perspectives]

Fantes, P. A., Hoffman, C. S.


Since its humble start as a model organism in two European laboratories in the 1940s and 1950s, the fission yeast Schizosaccharomyces pombe has grown to become one of the best-studied eukaryotes today. This article outlines the way in which interest in S. pombe developed and spread from Europe to Japan, North America, and elsewhere from its beginnings up to the first International Meeting devoted to this yeast in 1999. We describe the expansion of S. pombe research during this period with an emphasis on many of the individual researchers involved and their interactions that resulted in the development of today’s vibrant community.



Monday, June 6 2016 09:44:53 AM

Learning and Doing: An Interview with Bill Wood [The 2016 GSA Honors and Awards]

Wood, W. B.


THE Genetics Society of America’s Elizabeth W. Jones Award for Excellence in Education recognizes significant and sustained impact on genetics education. As well as having made major contributions to biochemistry and developmental genetics, the 2016 awardee William B. Wood has been a pioneer in the reform of science teaching. Wood’s leadership has been crucial in several national initiatives and programs, including the development of the influential National Academies Summer institutes on Undergraduate Education in Biology. He has also catalyzed change in education through his service as Editor-in-Chief of CBE-Life Sciences Education, a peer-reviewed journal published by the American Society for Cell Biology, in editorial partnership with the GSA.



Monday, June 6 2016 09:44:53 AM

Tools for Predicting the Functional Impact of Nonsynonymous Genetic Variation [Review]

Tang, H., Thomas, P. D.


As personal genome sequencing becomes a reality, understanding the effects of genetic variants on phenotype—particularly the impact of germline variants on disease risk and the impact of somatic variants on cancer development and treatment—continues to increase in importance. Because of their clear potential for affecting phenotype, nonsynonymous genetic variants (variants that cause a change in the amino acid sequence of a protein encoded by a gene) have long been the target of efforts to predict the effects of genetic variation. Whole-genome sequencing is identifying large numbers of nonsynonymous variants in each genome, intensifying the need for computational methods that accurately predict which of these are likely to impact disease phenotypes. This review focuses on nonsynonymous variant prediction with two aims in mind: (1) to review the prioritization methods that have been developed to date and the principles on which they are based and (2) to discuss the challenges to further improving these methods.



Monday, June 6 2016 09:44:53 AM

Tetrahymena as a Unicellular Model Eukaryote: Genetic and Genomic Tools [Genetic Toolbox]

Ruehle, M. D., Orias, E., Pearson, C. G.


Tetrahymena thermophila is a ciliate model organism whose study has led to important discoveries and insights into both conserved and divergent biological processes. In this review, we describe the tools for the use of Tetrahymena as a model eukaryote, including an overview of its life cycle, orientation to its evolutionary roots, and methodological approaches to forward and reverse genetics. Recent genomic tools have expanded Tetrahymena’s utility as a genetic model system. With the unique advantages that Tetrahymena provide, we argue that it will continue to be a model organism of choice.



Monday, June 6 2016 09:44:53 AM

Sgs1 and Mph1 Helicases Enforce the Recombination Execution Checkpoint During DNA Double-Strand Break Repair in Saccharomyces cerevisiae [Communications]

Jain, S., Sugawara, N., Mehta, A., Ryu, T., Haber, J. E.


We have previously shown that a recombination execution checkpoint (REC) regulates the choice of the homologous recombination pathway used to repair a given DNA double-strand break (DSB) based on the homology status of the DSB ends. If the two DSB ends are synapsed with closely-positioned and correctly-oriented homologous donors, repair proceeds rapidly by the gene conversion (GC) pathway. If, however, homology to only one of the ends is present, or if homologies to the two ends are situated far away from each other or in the wrong orientation, REC blocks the rapid initiation of new DNA synthesis from the synapsed end(s) and repair is carried out by the break-induced replication (BIR) machinery after a long pause. Here we report that the simultaneous deletion of two 3'->5' helicases, Sgs1 and Mph1, largely abolishes the REC-mediated lag normally observed during the repair of large gaps and BIR substrates, which now get repaired nearly as rapidly and efficiently as GC substrates. Deletion of SGS1 and MPH1 also produces a nearly additive increase in the efficiency of both BIR and long gap repair; this increase is epistatic to that seen upon Rad51 overexpression. However, Rad51 overexpression fails to mimic the acceleration in repair kinetics that is produced by sgs1 mph1 double deletion.



Monday, June 6 2016 09:44:53 AM

Evolution of Schooling Behavior in Threespine Sticklebacks Is Shaped by the Eda Gene [Communications]

Greenwood, A. K., Mills, M. G., Wark, A. R., Archambeault, S. L., Peichel, C. L.


Despite longstanding interest in the genetic mechanisms that underlie behavioral evolution, very few genes that underlie naturally occurring variation in behavior between individuals or species are known, particularly in vertebrates. Here, we build on our previous forward genetic mapping experiments and use transgenic approaches to identify Ectodysplasin as a gene that causes differences in schooling behavior between wild populations of threespine stickleback (Gasterosteus aculeatus) fish. This work provides rare insight into the proximate mechanisms that have shaped the evolution of vertebrate behavior.



Monday, June 6 2016 09:44:53 AM

Accurate Profiling of Gene Expression and Alternative Polyadenylation with Whole Transcriptome Termini Site Sequencing (WTTS-Seq) [Methods, Technology, and Resources]

Zhou, X., Li, R., Michal, J. J., Wu, X.-L., Liu, Z., Zhao, H., Xia, Y., Du, W., Wildung, M. R., Pouchnik, D. J., Harland, R. M., Jiang, Z.


Construction of next-generation sequencing (NGS) libraries involves RNA manipulation, which often creates noisy, biased, and artifactual data that contribute to errors in transcriptome analysis. In this study, a total of 19 whole transcriptome termini site sequencing (WTTS-seq) and seven RNA sequencing (RNA-seq) libraries were prepared from Xenopus tropicalis adult and embryo samples to determine the most effective library preparation method to maximize transcriptomics investigation. We strongly suggest that appropriate primers/adaptors are designed to inhibit amplification detours and that PCR overamplification is minimized to maximize transcriptome coverage. Furthermore, genome annotation must be improved so that missing data can be recovered. In addition, a complete understanding of sequencing platforms is critical to limit the formation of false-positive results. Technically, the WTTS-seq method enriches both poly(A)+ RNA and complementary DNA, adds 5'- and 3'-adaptors in one step, pursues strand sequencing and mapping, and profiles both gene expression and alternative polyadenylation (APA). Although RNA-seq is cost prohibitive, tends to produce false-positive results, and fails to detect APA diversity and dynamics, its combination with WTTS-seq is necessary to validate transcriptome-wide APA.



Monday, June 6 2016 09:44:53 AM

Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples [Methods, Technology, and Resources]

Snyder-Mackler, N., Majoros, W. H., Yuan, M. L., Shaver, A. O., Gordon, J. B., Kopp, G. H., Schlebusch, S. A., Wall, J. D., Alberts, S. C., Mukherjee, S., Zhou, X., Tung, J.


Research on the genetics of natural populations was revolutionized in the 1990s by methods for genotyping noninvasively 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 noninvasively 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 noninvasive samples are available. The lab protocol and software ("WHODAD") are freely available at www.tung-lab.org/protocols-and-software.html and www.xzlab.org/software.html, respectively.



Monday, June 6 2016 09:44:53 AM

Powerful and Adaptive Testing for Multi-trait and Multi-SNP Associations with GWAS and Sequencing Data [Statistical Genetics and Genomics]

Kim, J., Zhang, Y., Pan, W., for the Alzheimer's Disease Neuroimaging Initiative


Testing for genetic association with multiple traits has become increasingly important, not only because of its potential to boost statistical power, but also for its direct relevance to applications. For example, there is accumulating evidence showing that some complex neurodegenerative and psychiatric diseases like Alzheimer’s disease are due to disrupted brain networks, for which it would be natural to identify genetic variants associated with a disrupted brain network, represented as a set of multiple traits, one for each of multiple brain regions of interest. In spite of its promise, testing for multivariate trait associations is challenging: if not appropriately used, its power can be much lower than testing on each univariate trait separately (with a proper control for multiple testing). Furthermore, differing from most existing methods for single-SNP–multiple-trait associations, we consider SNP set-based association testing to decipher complicated joint effects of multiple SNPs on multiple traits. Because the power of a test critically depends on several unknown factors such as the proportions of associated SNPs and of traits, we propose a highly adaptive test at both the SNP and trait levels, giving higher weights to those likely associated SNPs and traits, to yield high power across a wide spectrum of situations. We illuminate relationships among the proposed and some existing tests, showing that the proposed test covers several existing tests as special cases. We compare the performance of the new test with that of several existing tests, using both simulated and real data. The methods were applied to structural magnetic resonance imaging data drawn from the Alzheimer’s Disease Neuroimaging Initiative to identify genes associated with gray matter atrophy in the human brain default mode network (DMN). For genome-wide association studies (GWAS), genes AMOTL1 on chromosome 11 and APOE on chromosome 19 were discovered by the new test to be significantly associated with the DMN. Notably, gene AMOTL1 was not detected by single SNP-based analyses. To our knowledge, AMOTL1 has not been highlighted in other Alzheimer’s disease studies before, although it was indicated to be related to cognitive impairment. The proposed method is also applicable to rare variants in sequencing data and can be extended to pathway analysis.



Monday, June 6 2016 09:44:53 AM

Nuclear Envelope Retention of LINC Complexes Is Promoted by SUN-1 Oligomerization in the Caenorhabditis elegans Germ Line [Genome Integrity and Transmission]

Daryabeigi, A., Woglar, A., Baudrimont, A., Silva, N., Paouneskou, D., Vesely, C., Rauter, M., Penkner, A., Jantsch, M., Jantsch, V.


SUN (Sad1 and UNC-84) and KASH (Klarsicht, ANC-1, and Syne homology) proteins are constituents of the inner and outer nuclear membranes. They interact in the perinuclear space via C-terminal SUN-KASH domains to form the linker of nucleoskeleton and cytoskeleton (LINC) complex thereby bridging the nuclear envelope. LINC complexes mediate numerous biological processes by connecting chromatin with the cytoplasmic force-generating machinery. Here we show that the coiled-coil domains of SUN-1 are required for oligomerization and retention of the protein in the nuclear envelope, especially at later stages of female gametogenesis. Consistently, deletion of the coiled-coil domain makes SUN-1 sensitive to unilateral force exposure across the nuclear membrane. Premature loss of SUN-1 from the nuclear envelope leads to embryonic death due to loss of centrosome–nuclear envelope attachment. However, in contrast to previous notions we can show that the coiled-coil domain is dispensable for functional LINC complex formation, exemplified by successful chromosome sorting and synapsis in meiotic prophase I in its absence.



Monday, June 6 2016 09:44:53 AM

Collaborative Control of Cell Cycle Progression by the RNA Exonuclease Dis3 and Ras Is Conserved Across Species [Cellular Genetics]

Snee, M. J., Wilson, W. C., Zhu, Y., Chen, S.-Y., Wilson, B. A., Kseib, C., ONeal, J., Mahajan, N., Tomasson, M. H., Arur, S., Skeath, J. B.


Dis3 encodes a conserved RNase that degrades or processes all RNA species via an N-terminal PilT N terminus (PIN) domain and C-terminal RNB domain that harbor, respectively, endonuclease activity and 3'–5' exonuclease activity. In Schizosaccharomyces pombe, dis3 mutations cause chromosome missegregation and failure in mitosis, suggesting dis3 promotes cell division. In humans, apparently hypomorphic dis3 mutations are found recurrently in multiple myeloma, suggesting dis3 opposes cell division. Except for the observation that RNAi-mediated depletion of dis3 function drives larval arrest and reduces tissue growth in Drosophila, the role of dis3 has not been rigorously explored in higher eukaryotic systems. Using the Drosophila system and newly generated dis3 null alleles, we find that absence of dis3 activity inhibits cell division. We uncover a conserved CDK1 phosphorylation site that when phosphorylated inhibits Dis3’s exonuclease, but not endonuclease, activity. Leveraging this information, we show that Dis3’s exonuclease function is required for mitotic cell division: in its absence, cells are delayed in mitosis and exhibit aneuploidy and overcondensed chromosomes. In contrast, we find that modest reduction of dis3 function enhances cell proliferation in the presence of elevated Ras activity, apparently by accelerating cells through G2/M even though each insult by itself delays G2/M. Additionally, we find that dis3 and ras genetically interact in worms and that dis3 can enhance cell proliferation under growth stimulatory conditions in murine B cells. Thus, reduction, but not absence, of dis3 activity can enhance cell proliferation in higher organisms.



Monday, June 6 2016 09:44:53 AM

Penetrance of Congenital Heart Disease in a Mouse Model of Down Syndrome Depends on a Trisomic Potentiator of a Disomic Modifier [Developmental and Behavioral Genetics]

Li, H., Edie, S., Klinedinst, D., Jeong, J. S., Blackshaw, S., Maslen, C. L., Reeves, R. H.


Down syndrome (DS) is a significant risk factor for congenital heart disease (CHD), increasing the incidence 50 times over the general population. However, half of people with DS have a normal heart and thus trisomy 21 is not sufficient to cause CHD by itself. Ts65Dn mice are trisomic for orthologs of >100 Hsa21 genes, and their heart defect frequency is significantly higher than their euploid littermates. Introduction of a null allele of Creld1 into Ts65Dn increases the penetrance of heart defects significantly. However, this increase was not seen when the Creld1 null allele was introduced into Ts1Cje, a mouse that is trisomic for about two thirds of the Hsa21 orthologs that are triplicated in Ts65Dn. Among the 23 genes present in three copies in Ts65Dn but not Ts1Cje, we identified Jam2 as necessary for the increased penetrance of Creld1-mediated septal defects in Ts65Dn. Thus, overexpression of the trisomic gene, Jam2, is a necessary potentiator of the disomic genetic modifier, Creld1. No direct physical interaction between Jam2 and Creld1 was identified by several methods. Regions of Hsa21 containing genes that are risk factors of CHD have been identified, but Jam2 (and its environs) has not been linked to heart formation previously. The complexity of this interaction may be more representative of the clinical situation in people than consideration of simple single-gene models.



Monday, June 6 2016 09:44:53 AM

Unexpected Roles for Ciliary Kinesins and Intraflagellar Transport Proteins [Developmental and Behavioral Genetics]

Pooranachandran, N., Malicki, J. J.


Transport of proteins in the ciliary shaft is driven by microtubule-dependent motors, kinesins. Prior studies suggested that the heterotrimeric ciliary kinesin may be dispensable for certain aspects of transport in specialized cilia of vertebrate photoreceptor cells. To test this possibility further, we analyzed the mutant phenotype of the zebrafish kif3a gene, which encodes the common motor subunit of heterotrimeric ciliary kinesins. Cilia are absent in all organs examined, leading to the conclusion that kif3a is indispensable for ciliogenesis in all cells, including photoreceptors. Unexpectedly, kif3a function precedes ciliogenesis as ciliary basal bodies are mispositioned in mutant photoreceptors. This phenotype is much less pronounced in intraflagellar transport (IFT) mutants and reveals that kif3a has a much broader role than previously assumed. Despite the severity of their basal body phenotype, kif3a mutant photoreceptors survive longer compared to those in IFT mutants, which display much weaker basal body mispositioning. This effect is absent in kif3a;IFT double mutants, indicating that IFT proteins have ciliary transport-independent roles, which add to the severity of their photoreceptor phenotype. kif3a is dispensable for basal body docking in otic vesicle sensory epithelia and, surprisingly, short cilia form in mechanosensory cristae even in the absence of kif3a. In contrast to Kif3a, the functions of the Kif3c-related protein, encoded by the kif3c-like (kif3cl) gene, and the homodimeric ciliary kinesin, kif17, are dispensable for photoreceptor morphogenesis. These studies demonstrate unexpected new roles for both ciliary heterotrimeric kinesins and IFT particle genes and clarify the function of kif17, the homodimeric ciliary kinesin gene.



Monday, June 6 2016 09:44:53 AM

Timing of Locomotor Recovery from Anoxia Modulated by the white Gene in Drosophila [Developmental and Behavioral Genetics]

Xiao, C., Robertson, R. M.


Locomotor recovery from anoxia follows the restoration of disordered ion distributions and neuronal excitability. The time taken for locomotor recovery after 30 sec anoxia (around 10 min) is longer than the time for the propagation of action potentials to be restored (<1 min) in Drosophila wild type. We report here that the white (w) gene modulates the timing of locomotor recovery. Wild-type flies displayed fast and consistent recovery of locomotion from anoxia, whereas mutants of w showed significantly delayed and more variable recovery. Genetic analysis including serial backcrossing revealed a strong association between the w locus and the timing of locomotor recovery, and haplo-insufficient function of w+ in promoting fast recovery. The locomotor recovery phenotype was independent of classic eye pigmentation, although both are associated with the w gene. Introducing up to four copies of mini-white (mw+) into w1118 was insufficient to promote fast and consistent locomotor recovery. However, flies carrying w+ duplicated to the Y chromosome showed wild-type-like fast locomotor recovery. Furthermore, Knockdown of w by RNA interference (RNAi) in neurons but not glia delayed locomotor recovery, and specifically, knockdown of w in subsets of serotonin neurons was sufficient to delay the locomotor recovery. These data reveal an additional role for w in modulating the timing of locomotor recovery from anoxia.



Monday, June 6 2016 09:44:53 AM

The Deadbeat Paternal Effect of Uncapped Sperm Telomeres on Cell Cycle Progression and Chromosome Behavior in Drosophila melanogaster [Developmental and Behavioral Genetics]

Yamaki, T., Yasuda, G. K., Wakimoto, B. T.


Telomere-capping complexes (TCCs) protect the ends of linear chromosomes from illegitimate repair and end-to-end fusions and are required for genome stability. The identity and assembly of TCC components have been extensively studied, but whether TCCs require active maintenance in nondividing cells remains an open question. Here we show that Drosophila melanogaster requires Deadbeat (Ddbt), a sperm nuclear basic protein (SNBP) that is recruited to the telomere by the TCC and is required for TCC maintenance during genome-wide chromatin remodeling, which transforms spermatids to mature sperm. Ddbt-deficient males produce sperm lacking TCCs. Their offspring delay the initiation of anaphase as early as cycle 1 but progress through the first two cycles. Persistence of uncapped paternal chromosomes induces arrest at or around cycle 3. This early arrest can be rescued by selective elimination of paternal chromosomes and production of gynogenetic haploid or haploid mosaics. Progression past cycle 3 can also occur if embryos have reduced levels of the maternally provided checkpoint kinase Chk2. The findings provide insights into how telomere integrity affects the regulation of the earliest embryonic cell cycles. They also suggest that other SNBPs, including those in humans, may have analogous roles and manifest as paternal effects on embryo quality.



Monday, June 6 2016 09:44:53 AM

Cross-Talk Between Sporophyte and Gametophyte Generations Is Promoted by CHD3 Chromatin Remodelers in Arabidopsis thaliana [Developmental and Behavioral Genetics]

Carter, B., Henderson, J. T., Svedin, E., Fiers, M., McCarthy, K., Smith, A., Guo, C., Bishop, B., Zhang, H., Riksen, T., Shockley, A., Dilkes, B. P., Boutilier, K., Ogas, J.


Angiosperm reproduction requires the integrated development of multiple tissues with different genotypes. To achieve successful fertilization, the haploid female gametophytes and diploid ovary must coordinate their development, after which the male gametes must navigate through the maternal sporophytic tissues to reach the female gametes. After fertilization, seed development requires coordinated development of the maternal diploid integuments, the triploid endosperm, and the diploid zygote. Transcription and signaling factors contribute to communication between these tissues, and roles for epigenetic regulation have been described for some of these processes. Here we identify a broad role for CHD3 chromatin remodelers in Arabidopsis thaliana reproductive development. Plants lacking the CHD3 remodeler, PICKLE, exhibit various reproductive defects including abnormal development of the integuments, female gametophyte, and pollen tube, as well as delayed progression of ovule and embryo development. Genetic analyses demonstrate that these phenotypes result from loss of PICKLE in the maternal sporophyte. The paralogous gene PICKLE RELATED 2 is preferentially expressed in the endosperm and acts antagonistically with respect to PICKLE in the seed: loss of PICKLE RELATED 2 suppresses the large seed phenotype of pickle seeds. Surprisingly, the alteration of seed size in pickle plants is sufficient to determine the expression of embryonic traits in the seedling primary root. These findings establish an important role for CHD3 remodelers in plant reproduction and highlight how the epigenetic status of one tissue can impact the development of genetically distinct tissues.



Monday, June 6 2016 09:44:53 AM

An Approximate Markov Model for the Wright-Fisher Diffusion and Its Application to Time Series Data [Population and Evolutionary Genetics]

Ferrer-Admetlla, A., Leuenberger, C., Jensen, J. D., Wegmann, D.


The joint and accurate inference of selection and demography from genetic data is considered a particularly challenging question in population genetics, since both process may lead to very similar patterns of genetic diversity. However, additional information for disentangling these effects may be obtained by observing changes in allele frequencies over multiple time points. Such data are common in experimental evolution studies, as well as in the comparison of ancient and contemporary samples. Leveraging this information, however, has been computationally challenging, particularly when considering multilocus data sets. To overcome these issues, we introduce a novel, discrete approximation for diffusion processes, termed mean transition time approximation, which preserves the long-term behavior of the underlying continuous diffusion process. We then derive this approximation for the particular case of inferring selection and demography from time series data under the classic Wright–Fisher model and demonstrate that our approximation is well suited to describe allele trajectories through time, even when only a few states are used. We then develop a Bayesian inference approach to jointly infer the population size and locus-specific selection coefficients with high accuracy and further extend this model to also infer the rates of sequencing errors and mutations. We finally apply our approach to recent experimental data on the evolution of drug resistance in influenza virus, identifying likely targets of selection and finding evidence for much larger viral population sizes than previously reported.



Monday, June 6 2016 09:44:54 AM

Epistasis and the Structure of Fitness Landscapes: Are Experimental Fitness Landscapes Compatible with Fishers Geometric Model? [Population and Evolutionary Genetics]

Blanquart, F., Bataillon, T.


The fitness landscape defines the relationship between genotypes and fitness in a given environment and underlies fundamental quantities such as the distribution of selection coefficient and the magnitude and type of epistasis. A better understanding of variation in landscape structure across species and environments is thus necessary to understand and predict how populations will adapt. An increasing number of experiments investigate the properties of fitness landscapes by identifying mutations, constructing genotypes with combinations of these mutations, and measuring the fitness of these genotypes. Yet these empirical landscapes represent a very small sample of the vast space of all possible genotypes, and this sample is often biased by the protocol used to identify mutations. Here we develop a rigorous statistical framework based on Approximate Bayesian Computation to address these concerns and use this flexible framework to fit a broad class of phenotypic fitness models (including Fisher’s model) to 26 empirical landscapes representing nine diverse biological systems. Despite uncertainty owing to the small size of most published empirical landscapes, the inferred landscapes have similar structure in similar biological systems. Surprisingly, goodness-of-fit tests reveal that this class of phenotypic models, which has been successful so far in interpreting experimental data, is a plausible in only three of nine biological systems. More precisely, although Fisher’s model was able to explain several statistical properties of the landscapes—including the mean and SD of selection and epistasis coefficients—it was often unable to explain the full structure of fitness landscapes.



Monday, June 6 2016 09:44:54 AM

Elevated Linkage Disequilibrium and Signatures of Soft Sweeps Are Common in Drosophila melanogaster [Population and Evolutionary Genetics]

Garud, N. R., Petrov, D. A.


The extent to which selection and demography impact patterns of genetic diversity in natural populations of Drosophila melanogaster is yet to be fully understood. We previously observed that linkage disequilibrium (LD) at scales of ~10 kb in the Drosophila Genetic Reference Panel (DGRP), consisting of 145 inbred strains from Raleigh, North Carolina, measured both between pairs of sites and as haplotype homozygosity, is elevated above neutral demographic expectations. We also demonstrated that signatures of strong and recent soft sweeps are abundant. However, the extent to which these patterns are specific to this derived and admixed population is unknown. It is also unclear whether these patterns are a consequence of the extensive inbreeding performed to generate the DGRP data. Here we analyze LD statistics in a sample of >100 fully-sequenced strains from Zambia; an ancestral population to the Raleigh population that has experienced little to no admixture and was generated by sequencing haploid embryos rather than inbred strains. We find an elevation in long-range LD and haplotype homozygosity compared to neutral expectations in the Zambian sample, thus showing the elevation in LD is not specific to the DGRP data set. This elevation in LD and haplotype structure remains even after controlling for possible confounders including genomic inversions, admixture, population substructure, close relatedness of individual strains, and recombination rate variation. Furthermore, signatures of partial soft sweeps similar to those found in the DGRP as well as partial hard sweeps are common in Zambia. These results suggest that while the selective forces and sources of adaptive mutations may differ in Zambia and Raleigh, elevated long-range LD and signatures of soft sweeps are generic in D. melanogaster.



Monday, June 6 2016 09:44:54 AM

The Genetic Cost of Neanderthal Introgression [Population and Evolutionary Genetics]

Harris, K., Nielsen, R.


Approximately 2–4% of genetic material in human populations outside Africa is derived from Neanderthals who interbred with anatomically modern humans. Recent studies have shown that this Neanderthal DNA is depleted around functional genomic regions; this has been suggested to be a consequence of harmful epistatic interactions between human and Neanderthal alleles. However, using published estimates of Neanderthal inbreeding and the distribution of mutational fitness effects, we infer that Neanderthals had at least 40% lower fitness than humans on average; this increased load predicts the reduction in Neanderthal introgression around genes without the need to invoke epistasis. We also predict a residual Neanderthal mutational load in non-Africans, leading to a fitness reduction of at least 0.5%. This effect of Neanderthal admixture has been left out of previous debate on mutation load differences between Africans and non-Africans. We also show that if many deleterious mutations are recessive, the Neanderthal admixture fraction could increase over time due to the protective effect of Neanderthal haplotypes against deleterious alleles that arose recently in the human population. This might partially explain why so many organisms retain gene flow from other species and appear to derive adaptive benefits from introgression.



Monday, June 6 2016 09:44:54 AM

Likelihood-Free Inference in High-Dimensional Models [Population and Evolutionary Genetics]

Kousathanas, A., Leuenberger, C., Helfer, J., Quinodoz, M., Foll, M., Wegmann, D.


Methods that bypass analytical evaluations of the likelihood function have become an indispensable tool for statistical inference in many fields of science. These so-called likelihood-free methods rely on accepting and rejecting simulations based on summary statistics, which limits them to low-dimensional models for which the value of the likelihood is large enough to result in manageable acceptance rates. To get around these issues, we introduce a novel, likelihood-free Markov chain Monte Carlo (MCMC) method combining two key innovations: updating only one parameter per iteration and accepting or rejecting this update based on subsets of statistics approximately sufficient for this parameter. This increases acceptance rates dramatically, rendering this approach suitable even for models of very high dimensionality. We further derive that for linear models, a one-dimensional combination of statistics per parameter is sufficient and can be found empirically with simulations. Finally, we demonstrate that our method readily scales to models of very high dimensionality, using toy models as well as by jointly inferring the effective population size, the distribution of fitness effects (DFE) of segregating mutations, and selection coefficients for each locus from data of a recent experiment on the evolution of drug resistance in influenza.



Monday, June 6 2016 09:44:54 AM

Functional Divergence of the Nuclear Receptor NR2C1 as a Modulator of Pluripotentiality During Hominid Evolution [Population and Evolutionary Genetics]

Baker, J. L., Dunn, K. A., Mingrone, J., Wood, B. A., Karpinski, B. A., Sherwood, C. C., Wildman, D. E., Maynard, T. M., Bielawski, J. P.


Genes encoding nuclear receptors (NRs) are attractive as candidates for investigating the evolution of gene regulation because they (1) have a direct effect on gene expression and (2) modulate many cellular processes that underlie development. We employed a three-phase investigation linking NR molecular evolution among primates with direct experimental assessment of NR function. Phase 1 was an analysis of NR domain evolution and the results were used to guide the design of phase 2, a codon-model-based survey for alterations of natural selection within the hominids. By using a series of reliability and robustness analyses we selected a single gene, NR2C1, as the best candidate for experimental assessment. We carried out assays to determine whether changes between the ancestral and extant NR2C1s could have impacted stem cell pluripotency (phase 3). We evaluated human, chimpanzee, and ancestral NR2C1 for transcriptional modulation of Oct4 and Nanog (key regulators of pluripotency and cell lineage commitment), promoter activity for Pepck (a proxy for differentiation in numerous cell types), and average size of embryological stem cell colonies (a proxy for the self-renewal capacity of pluripotent cells). Results supported the signal for alteration of natural selection identified in phase 2. We suggest that adaptive evolution of gene regulation has impacted several aspects of pluripotentiality within primates. Our study illustrates that the combination of targeted evolutionary surveys and experimental analysis is an effective strategy for investigating the evolution of gene regulation with respect to developmental phenotypes.



Monday, June 6 2016 09:44:54 AM

An Evolving Genetic Architecture Interacts with Hill-Robertson Interference to Determine the Benefit of Sex [Population and Evolutionary Genetics]

Whitlock, A. O. B., Peck, K. M., Azevedo, R. B. R., Burch, C. L.


Sex is ubiquitous in the natural world, but the nature of its benefits remains controversial. Previous studies have suggested that a major advantage of sex is its ability to eliminate interference between selection on linked mutations, a phenomenon known as Hill–Robertson interference. However, those studies may have missed both important advantages and important disadvantages of sexual reproduction because they did not allow the distributions of mutational effects and interactions (i.e., the genetic architecture) to evolve. Here we investigate how Hill–Robertson interference interacts with an evolving genetic architecture to affect the evolutionary origin and maintenance of sex by simulating evolution in populations of artificial gene networks. We observed a long-term advantage of sex—equilibrium mean fitness of sexual populations exceeded that of asexual populations—that did not depend on population size. We also observed a short-term advantage of sex—sexual modifier mutations readily invaded asexual populations—that increased with population size, as was observed in previous studies. We show that the long- and short-term advantages of sex were both determined by differences between sexual and asexual populations in the evolutionary dynamics of two properties of the genetic architecture: the deleterious mutation rate ($${U}_{\mathrm{d}}$$) and recombination load ($${L}_{\mathrm{R}}$$). These differences resulted from a combination of selection to minimize $${L}_{\mathrm{R}},$$ which is experienced only by sexuals, and Hill–Robertson interference experienced primarily by asexuals. In contrast to the previous studies, in which Hill–Robertson interference had only a direct impact on the fitness advantages of sex, the impact of Hill–Robertson interference in our simulations was mediated additionally by an indirect impact on the efficiency with which selection acted to reduce $${U}_{\mathrm{d}}.$$



Monday, June 6 2016 09:44:54 AM

Background Selection in Partially Selfing Populations [Population and Evolutionary Genetics]

Roze, D.


Self-fertilizing species often present lower levels of neutral polymorphism than their outcrossing relatives. Indeed, selfing automatically increases the rate of coalescence per generation, but also enhances the effects of background selection and genetic hitchhiking by reducing the efficiency of recombination. Approximations for the effect of background selection in partially selfing populations have been derived previously, assuming tight linkage between deleterious alleles and neutral loci. However, loosely linked deleterious mutations may have important effects on neutral diversity in highly selfing populations. In this article, I use a general method based on multilocus population genetics theory to express the effect of a deleterious allele on diversity at a linked neutral locus in terms of moments of genetic associations between loci. Expressions for these genetic moments at equilibrium are then computed for arbitrary rates of selfing and recombination. An extrapolation of the results to the case where deleterious alleles segregate at multiple loci is checked using individual-based simulations. At high selfing rates, the tight linkage approximation underestimates the effect of background selection in genomes with moderate to high map length; however, another simple approximation can be obtained for this situation and provides accurate predictions as long as the deleterious mutation rate is not too high.



Monday, June 6 2016 09:44:54 AM

Limits to Adaptation in Partially Selfing Species [Population and Evolutionary Genetics]

Hartfield, M., Glemin, S.


In outcrossing populations, "Haldane’s sieve" states that recessive beneficial alleles are less likely to fix than dominant ones, because they are less exposed to selection when rare. In contrast, selfing organisms are not subject to Haldane’s sieve and are more likely to fix recessive types than outcrossers, as selfing rapidly creates homozygotes, increasing overall selection acting on mutations. However, longer homozygous tracts in selfers also reduce the ability of recombination to create new genotypes. It is unclear how these two effects influence overall adaptation rates in partially selfing organisms. Here, we calculate the fixation probability of beneficial alleles if there is an existing selective sweep in the population. We consider both the potential loss of the second beneficial mutation if it has a weaker advantage than the first one, and the possible replacement of the initial allele if the second mutant is fitter. Overall, loss of weaker adaptive alleles during a first selective sweep has a larger impact on preventing fixation of both mutations in highly selfing organisms. Furthermore, the presence of linked mutations has two opposing effects on Haldane’s sieve. First, recessive mutants are disproportionally likely to be lost in outcrossers, so it is likelier that dominant mutations will fix. Second, with elevated rates of adaptive mutation, selective interference annuls the advantage in selfing organisms of not suffering from Haldane’s sieve; outcrossing organisms are more able to fix weak beneficial mutations of any dominance value. Overall, weakened recombination effects can greatly limit adaptation in selfing organisms.



Monday, June 6 2016 09:44:54 AM

Inferring the Frequency Spectrum of Derived Variants to Quantify Adaptive Molecular Evolution in Protein-Coding Genes of Drosophila melanogaster [Population and Evolutionary Genetics]

Keightley, P. D., Campos, J. L., Booker, T. R., Charlesworth, B.


Many approaches for inferring adaptive molecular evolution analyze the unfolded site frequency spectrum (SFS), a vector of counts of sites with different numbers of copies of derived alleles in a sample of alleles from a population. Accurate inference of the high-copy-number elements of the SFS is difficult, however, because of misassignment of alleles as derived vs. ancestral. This is a known problem with parsimony using outgroup species. Here we show that the problem is particularly serious if there is variation in the substitution rate among sites brought about by variation in selective constraint levels. We present a new method for inferring the SFS using one or two outgroups that attempts to overcome the problem of misassignment. We show that two outgroups are required for accurate estimation of the SFS if there is substantial variation in selective constraints, which is expected to be the case for nonsynonymous sites in protein-coding genes. We apply the method to estimate unfolded SFSs for synonymous and nonsynonymous sites in a population of Drosophila melanogaster from phase 2 of the Drosophila Population Genomics Project. We use the unfolded spectra to estimate the frequency and strength of advantageous and deleterious mutations and estimate that ~50% of amino acid substitutions are positively selected but that <0.5% of new amino acid mutations are beneficial, with a scaled selection strength of Nes 12.



Monday, June 6 2016 09:44:54 AM

Transcript Isoform Variation Associated with Cytosine Modification in Human Lymphoblastoid Cell Lines [Genome and Systems Biology]

Zhang, X., Zhang, W.


Cytosine modification on DNA is variable among individuals, which could correlate with gene expression variation. The effect of cytosine modification on interindividual transcript isoform variation (TIV), however, remains unclear. In this study, we assessed the extent of cytosine modification-specific TIV in lymphoblastoid cell lines (LCLs) derived from unrelated individuals of European and African descent. Our study detected cytosine modification-specific TIVs for 17% of the analyzed genes at a 5% false discovery rate. Forty-five percent of the TIV-associated cytosine modifications correlated with the overall gene expression levels as well, with the corresponding CpG sites overrepresented in transcript initiation sites, transcription factor binding sites, and distinct histone modification peaks, suggesting that alternative isoform transcription underlies the TIVs. Our analysis also revealed 33% of the TIV-associated cytosine modifications that affected specific exons, with the corresponding CpG sites overrepresented in exon/intron junctions, splicing branching points, and transcript termination sites, implying that the TIVs are attributable to alternative splicing or transcription termination. Genetic and epigenetic regulation of TIV shared target preference but exerted independent effects on 61% of the common exon targets. Cytosine modification-specific TIVs detected from LCLs were differentially enriched in those detected from various tissues in The Cancer Genome Atlas, indicating their developmental dependency. Genes containing cytosine modification-specific TIVs were enriched in pathways of cancers and metabolic disorders. Our study demonstrated a prominent effect of cytosine modification variation on the transcript isoform spectrum over gross transcript abundance and revealed epigenetic contributions to diseases that were mediated through cytosine modification-specific TIV.



Monday, June 6 2016 09:44:54 AM

Corrigendum [Corrigendum]


Monday, June 6 2016 09:44:54 AM

Corrigendum [Corrigendum]