bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of Heading Date Quantitative Trait Locus Hd6 and Characterization of Its Epistatic Interactions With Hd2 in Rice Using Advanced Backcross Progeny
Authors: Yamamoto Toshio , Lin Hongxuan , Sasaki Takuji , Yano Masahiro
Published: April 2021

A backcrossed population (BC4F2) derived from a cross between a japonica rice variety, Nipponbare, as the recurrent parent and an indica rice variety, Kasalath, as the donor parent showed a long-range variation in days to heading. Quantitative trait loci (QTL) analysis revealed that two QTL, one on chromosome 3, designated Hd6, and another on chromosome 2, designated Hd7, were involved in this variation; and Hd6 was precisely mapped as a single Mendelian factor by using progeny testing (BC4F3). The nearly isogenic line with QTL (QTL-NIL) that carries the chromosomal segment from Kasalath for the Hd6 region in Nipponbare's genetic background was developed by marker-assisted selection. In a day-length treatment test, the QTL-NIL for Hd6 prominently increased days to heading under a 13.5-hr day length compared with the recurrent parent, Nipponbare, suggesting that Hd6 controls photoperiod sensitivity. QTL analysis of the F2 population derived from a cross between the QTL-NILs revealed existence of an epistatic interaction between Hd2, which is one of the photoperiod sensitivity genes detected in a previous analysis, and Hd6. The day-length treatment tests of these QTL-NILs, including the line introgressing both Hd2 and Hd6, also indicated an epistatic interaction for photoperiod sensitivity between them.
Estimation of Population Parameters and Recombination Rates From Single Nucleotide Polymorphisms
Authors: Nielsen Rasmus
Published: April 2021

Some general likelihood and Bayesian methods for analyzing single nucleotide polymorphisms (SNPs) are presented. First, an efficient method for estimating demographic parameters from SNPs in linkage equilibrium is derived. The method is applied in the estimation of growth rates of a human population based on 37 SNP loci. It is demonstrated how ascertainment biases, due to biased sampling of loci, can be avoided, at least in some cases, by appropriate conditioning when calculating the likelihood function. Second, a Markov chain Monte Carlo (MCMC) method for analyzing linked SNPs is developed. This method can be used for Bayesian and likelihood inference on linked SNPs. The utility of the method is illustrated by estimating recombination rates in a human data set containing 17 SNPs and 60 individuals. Both methods are based on assumptions of low mutation rates.
Subtelomeric Repeat Amplification Is Associated With Growth at Elevated Temperature in yku70 Mutants of Saccharomyces cerevisiae
Authors: Fellerhoff Barbara , Eckardt-Schupp Friederike , Friedl Anna A
Published: April 2021

Inactivation of the Saccharomyces cerevisiae gene YKU70 (HDF1), which encodes one subunit of the Ku heterodimer, confers a DNA double-strand break repair defect, shortening of and structural alterations in the telomeres, and a severe growth defect at 37°. To elucidate the basis of the temperature sensitivity, we analyzed subclones derived from rare yku70 mutant cells that formed a colony when plated at elevated temperature. In all these temperature-resistant subclones, but not in cell populations shifted to 37°, we observed substantial amplification and redistribution of subtelomeric Y′ element DNA. Amplification of Y′ elements and adjacent telomeric sequences has been described as an alternative pathway for chromosome end stabilization that is used by postsenescence survivors of mutants deficient for the telomerase pathway. Our data suggest that the combination of Ku deficiency and elevated temperature induces a potentially lethal alteration of telomere structure or function. Both in yku70 mutants and in wild type, incubation at 37° results in a slight reduction of the mean length of terminal restriction fragments, but not in a significant loss of telomeric (C1-3A/TG1-3)n sequences. We propose that the absence of Ku, which is known to bind to telomeres, affects the telomeric chromatin so that its chromosome end-defining function is lost at 37°.
Trinucleotide Repeats Are Clustered in Regulatory Genes in Saccharomyces cerevisiae
Authors: Young Elton T , Sloan James S , Van Riper Kristen
Published: April 2021

The genome of Saccharomyces cerevisiae contains numerous unstable microsatellite sequences. Mononucleotide and dinucleotide repeats are rarely found in ORFs, and when present in an ORF are frequently located in an intron or at the C terminus of the protein, suggesting that their instability is deleterious to gene function. DNA trinucleotide repeats (TNRs) are found at a higher-than-expected frequency within ORFs, and the amino acids encoded by the TNRs represent a biased set. TNRs are rarely conserved between genes with related sequences, suggesting high instability or a recent origin. The genes in which TNRs are most frequently found are related to cellular regulation. The protein structural database is notably lacking in proteins containing amino acid tracts, suggesting that they are not located in structured regions of a protein but are rather located between domains. This conclusion is consistent with the location of amino acid tracts in two protein families. The preferred location of TNRs within the ORFs of genes related to cellular regulation together with their instability suggest that TNRs could have an important role in speciation. Specifically, TNRs could serve as hot spots for recombination leading to domain swapping, or mutation of TNRs could allow rapid evolution of new domains of protein structure.
Effects of Colonization Processes on Genetic Diversity: Differences Between Annual Plants and Tree Species
Authors: Austerlitz Frédéric , Mariette Stéphanie , Machon Nathalie , Gouyon Pierre-Henri , Godelle Bernard
Published: April 2021

Tree species are striking for their high within-population diversity and low among-population differentiation for nuclear genes. In contrast, annual plants show much more differentiation for nuclear genes but much less diversity than trees. The usual explanation for this difference is that pollen flow, and therefore gene flow, is much higher for trees. This explanation is problematic because it relies on equilibrium hypotheses. Because trees have very recently recolonized temperate areas, they have experienced many foundation events, which usually reduce within-population diversity and increase differentiation. Only extremely high levels of gene flow could counterbalance these successive founder effects. We develop a model to study the impact of life cycle of forest trees, in particular of the length of their juvenile phase, on genetic diversity and differentiation during the glacial period and the following colonization period. We show that both a reasonably high level of pollen flow and the life-cycle characteristics of trees are needed to explain the observed structure of genetic diversity. We also show that gene flow and life cycle both have an impact on maternally inherited cytoplasmic genes, which are characterized both in trees and annual species by much less diversity and much more differentiation than nuclear genes.
Understanding the Overdispersed Molecular Clock
Authors: Cutler David J
Published: April 2021

Rates of molecular evolution at some protein-encoding loci are more irregular than expected under a simple neutral model of molecular evolution. This pattern of excessive irregularity in protein substitutions is often called the “overdispersed molecular clock” and is characterized by an index of dispersion, R(T) > 1. Assuming infinite sites, no recombination model of the gene R(T) is given for a general stationary model of molecular evolution. R(T) is shown to be affected by only three things: fluctuations that occur on a very slow time scale, advantageous or deleterious mutations, and interactions between mutations. In the absence of interactions, advantageous mutations are shown to lower R(T); deleterious mutations are shown to raise it. Previously described models for the overdispersed molecular clock are analyzed in terms of this work as are a few very simple new models. A model of deleterious mutations is shown to be sufficient to explain the observed values of R(T). Our current best estimates of R(T) suggest that either most mutations are deleterious or some key population parameter changes on a very slow time scale. No other interpretations seem plausible. Finally, a comment is made on how R(T) might be used to distinguish selective sweeps from background selection.
Genetic, Behavioral and Environmental Determinants of Male Longevity in Caenorhabditis elegans
Authors: Gems David , Riddle Donald L
Published: April 2021

Males of the nematode Caenorhabditis elegans are shorter lived than hermaphrodites when maintained in single-sex groups. We observed that groups of young males form clumps and that solitary males live longer, indicating that male-male interactions reduce life span. By contrast, grouped or isolated hermaphrodites exhibited the same longevity. In one wild isolate of C. elegans, AB2, there was evidence of copulation between males. Nine uncoordinated (unc) mutations were used to block clumping behavior. These mutations had little effect on hermaphrodite life span in most cases, yet many increased male longevity even beyond that of solitary wild-type males. In one case, the neuronal function mutant unc-64(e246), hermaphrodite life span was also increased by up to 60%. The longevity of unc-4(e120), unc-13(e51), and unc-32(e189) males exceeded that of hermaphrodites by 70–120%. This difference appears to reflect a difference in sex-specific life span potential revealed in the absence of male behavior that is detrimental to survival. The greater longevity of males appears not to be affected by daf-2, but is influenced by daf-16. In the absence of male-male interactions, median (but not maximum) male life span was variable. This variability was reduced when dead bacteria were used as food. Maintenance on dead bacteria extended both male and hermaphrodite longevity.
Neutral Evolution of the Sex-Determining Gene transformer in Drosophila
Authors: McAllister Bryant F , McVean Gilean A T
Published: April 2021

The amino acid sequence of the transformer (tra) gene exhibits an extremely rapid rate of evolution among Drosophila species, although the gene performs a critical step in sex determination. These changes in amino acid sequence are the result of either natural selection or neutral evolution. To differentiate between selective and neutral causes of this evolutionary change, analyses of both intraspecific and interspecific patterns of molecular evolution of tra gene sequences are presented. Sequences of 31 tra alleles were obtained from Drosophila americana. Many replacement and silent nucleotide variants are present among the alleles; however, the distribution of this sequence variation is consistent with neutral evolution. Sequence evolution was also examined among six species representative of the genus Drosophila. For most lineages and most regions of the gene, both silent and replacement substitutions have accumulated in a constant, clock-like manner. In exon 3 of D. virilis and D. americana we find evidence for an elevated rate of nonsynonymous substitution, but no statistical support for a greater rate of nonsynonymous relative to synonymous substitutions. Both levels of analysis of the tra sequence suggest that, although the gene is evolving at a rapid pace, these changes are neutral in function.
A Detailed Linkage Map of Medaka, Oryzias latipes: Comparative Genomics and Genome Evolution
Authors: Naruse Kiyoshi , Fukamachi Shoji , Mitani Hiroshi , Kondo Mariko , Matsuoka Tomoko , Kondo Shu , Hanamura Nana , Morita Yutaka , Hasegawa Kazuhito , Nishigaki Reiko , Shimada Atsuko , Wada Hironori , Kusakabe Takehiro , Suzuki Norio , Kinoshita Masato , Kanamori Akira , Terado Tokio , Kimura Hiroshi , Nonaka Masaru , Shima Akihiro
Published: April 2021

We mapped 633 markers (488 AFLPs, 28 RAPDs, 34 IRSs, 75 ESTs, 4 STSs, and 4 phenotypic markers) for the Medaka Oryzias latipes, a teleost fish of the order Beloniformes. Linkage was determined using a reference typing DNA panel from 39 cell lines derived from backcross progeny. This panel provided unlimited DNA for the accumulation of mapping data. The total map length of Medaka was 1354.5 cM and 24 linkage groups were detected, corresponding to the haploid chromosome number of the organism. Thirteen to 49 markers for each linkage group were obtained. Conserved synteny between Medaka and zebrafish was observed for 2 independent linkage groups. Unlike zebrafish, however, the Medaka linkage map showed obvious restriction of recombination on the linkage group containing the male-determining region (Y) locus compared to the autosomal chromosomes.
Microsatellite Mutations and Inferences About Human Demography
Authors: Gonser Rusty , Donnelly Peter , Nicholson George , Di Rienzo Anna
Published: April 2021

Microsatellites have been widely used as tools for population studies. However, inference about population processes relies on the specification of mutation parameters that are largely unknown and likely to differ across loci. Here, we use data on somatic mutations to investigate the mutation process at 14 tetranucleotide repeats and carry out an advanced multilocus analysis of different demographic scenarios on worldwide population samples. We use a method based on less restrictive assumptions about the mutation process, which is more powerful to detect departures from the null hypothesis of constant population size than other methods previously applied to similar data sets. We detect a signal of population expansion in all samples examined, except for one African sample. As part of this analysis, we identify an “anomalous” locus whose extreme pattern of variation cannot be explained by variability in mutation size. Exaggerated mutation rate is proposed as a possible cause for its unusual variation pattern. We evaluate the effect of using it to infer population histories and show that inferences about demographic histories are markedly affected by its inclusion. In fact, exclusion of the anomalous locus reduces interlocus variability of statistics summarizing population variation and strengthens the evidence in favor of demographic growth.
A Compound Poisson Process for Relaxing the Molecular Clock
Authors: Huelsenbeck John P , Larget Bret , Swofford David
Published: April 2021

The molecular clock hypothesis remains an important conceptual and analytical tool in evolutionary biology despite the repeated observation that the clock hypothesis does not perfectly explain observed DNA sequence variation. We introduce a parametric model that relaxes the molecular clock by allowing rates to vary across lineages according to a compound Poisson process. Events of substitution rate change are placed onto a phylogenetic tree according to a Poisson process. When an event of substitution rate change occurs, the current rate of substitution is modified by a gamma-distributed random variable. Parameters of the model can be estimated using Bayesian inference. We use Markov chain Monte Carlo integration to evaluate the posterior probability distribution because the posterior probability involves high dimensional integrals and summations. Specifically, we use the Metropolis-Hastings-Green algorithm with 11 different move types to evaluate the posterior distribution. We demonstrate the method by analyzing a complete mtDNA sequence data set from 23 mammals. The model presented here has several potential advantages over other models that have been proposed to relax the clock because it is parametric and does not assume that rates change only at speciation events. This model should prove useful for estimating divergence times when substitution rates vary across lineages.
Drosophila wee1 Has an Essential Role in the Nuclear Divisions of Early Embryogenesis
Authors: Price Donald , Rabinovitch Simon , O'Farrell Patrick H , Campbell Shelagh D
Published: April 2021

In Drosophila, the maternally expressed mei-41 and grp genes are required for successful execution of the nuclear division cycles of early embryogenesis. In fission yeast, genes encoding similar kinases (rad3 and chk1, respectively) are components of a cell cycle checkpoint that delays mitosis by inhibitory phosphorylation of Cdk1. We have identified mutations in a gene encoding a Cdk1 inhibitory kinase, Drosophila wee1 (Dwee1). Like mei-41 and grp, Dwee1 is zygotically dispensable but is required maternally for completing the embryonic nuclear cycles. The arrest phenotype of Dwee1 mutants, as well as genetic interactions between Dwee1, grp, and mei-41 mutations, suggest that Dwee1 is functioning in the same regulatory pathway as these genes. These findings imply that inhibitory phosphorylation of Cdk1 by Dwee1 is required for proper regulation of the early syncytial cycles of embryogenesis.
Genetic Analysis of a Y-Chromosome Region That Induces Triplosterile Phenotypes and Is Essential for Spermatid Individualization in Drosophila melanogaster
Authors: Timakov Benjamin , Zhang Ping
Published: April 2021

The heterochromatic Y chromosome of Drosophila melanogaster contains ~40 Mb of DNA but has only six loci mutable to male sterility. Region h1-h9 on YL, which carries the kl-3 and kl-5 loci, induces male sterility when present in three copies. We show that three separate segments within the region are responsible for the triplosterility and have an additive effect on male fertility. The triplosterile males displayed pleiotropic defects, beginning at early postmeiotic stages. However, the triplosterility was unaffected by kl-3 or kl-5 alleles. These data suggest that region h1-h9 is complex and may contain novel functions in addition to those of the previously identified kl-3 and kl-5 loci. The kl-3 and kl-5 mutations as well as deficiencies within region h1-h9 result in loss of the spermatid axonemal outer dynein arms. Examination using fluorescent probes showed that males deficient for h1-h3 or h4-h9 displayed a postmeiotic lesion with disrupted individualization complexes scattered along the spermatid bundle. In contrast, the kl-3 and kl-5 mutations had no effect on spermatid individualization despite the defect in the axonemes. These results demonstrate that region h1-h9 carries genetically separable functions: one required for spermatid individualization and the other essential for assembling the axonemal dynein arms.
Two Independent Loci Control Agamospermy (Apomixis) in the Triploid Flowering Plant Erigeron annuus
Authors: Noyes Richard D , Rieseberg Loren H
Published: April 2021

Asexual seed production (agamospermy) via gametophytic apomixis in flowering plants typically involves the formation of an unreduced megagametophyte (via apospory or diplospory) and the parthenogenetic development of the unreduced egg cell into an embryo. Agamospermy is almost exclusively restricted to polyploids. In this study, the genetic basis of agamospermy was investigated in a segregating population of 130 F1's from a cross between triploid (2n = 27) agamospermous Erigeron annuus and sexual diploid (2n = 18) E. strigosus. Correlations between markers and phenotypes and linkage analysis were performed on 387 segregating amplified fragment length polymorphisms (AFLPs). Results show that four closely linked markers with polysomic inheritance are significantly associated with parthenogenesis and that 11 cosegregating markers with univalent inheritance are completely associated with diplospory. This indicates that diplospory and parthenogenesis are unlinked and inherited independently. Further, the absence of agamospermy in diploid F1's appears to be best explained by a combination of recessive-lethal gametophytic selection against the parthenogenetic locus and univalent inheritance of the region bearing diplospory. These results may have major implications for attempts to manipulate agamospermy for agricultural purposes and for interpreting the evolution of the trait.
Selective Mapping: A Strategy for Optimizing the Construction of High-Density Linkage Maps
Authors: Vision Todd J , Brown Daniel G , Shmoys David B , Durrett Richard T , Tanksley Steven D
Published: April 2021

Historically, linkage mapping populations have consisted of large, randomly selected samples of progeny from a given pedigree or cell lines from a panel of radiation hybrids. We demonstrate that, to construct a map with high genome-wide marker density, it is neither necessary nor desirable to genotype all markers in every individual of a large mapping population. Instead, a reduced sample of individuals bearing complementary recombinational or radiation-induced breakpoints may be selected for genotyping subsequent markers from a large, but sparsely genotyped, mapping population. Choosing such a sample can be reduced to a discrete stochastic optimization problem for which the goal is a sample with breakpoints spaced evenly throughout the genome. We have developed several different methods for selecting such samples and have evaluated their performance on simulated and actual mapping populations, including the Lister and Dean Arabidopsis thaliana recombinant inbred population and the GeneBridge 4 human radiation hybrid panel. Our methods quickly and consistently find much-reduced samples with map resolution approaching that of the larger populations from which they are derived. This approach, which we have termed selective mapping, can facilitate the production of high-quality, high-density genome-wide linkage maps.
Point Mutations Identify a Conserved Region of theSaccharomyces cerevisiae AFR1Gene That Is Essential for Both the Pheromone Signaling and Morphogenesis Functions
Authors: DeMattei Cordell R , Davis Colleen P , Konopka James B
Published: April 2021

Mating pheromone receptors activate a G protein signal pathway that leads to the conjugation of the yeast Saccharomyces cerevisiae. This pathway also induces the production of Afr1p, a protein that negatively regulates pheromone receptor signaling and is required to form pointed projections of new growth that become the site of cell fusion during mating. Afr1p lacks strong similarity to any well-characterized proteins to help predict how it acts. Therefore, we investigated the relationship between the different functions of Afr1p by isolating and characterizing seven mutants that were defective in regulating pheromone signaling. The AFR1 mutants were also defective when expressed as fusions to STE2, the α-factor receptor, indicating that the mutant Afr1 proteins are defective in function and not in co-localizing with receptors. The mutant genes contained four distinct point mutations that all occurred between codons 254 and 263, identifying a region that is critical for AFR1 function. Consistent with this, we found that the corresponding region is very highly conserved in the Afr1p homologs from the yeasts S. uvarum and S. douglasii. In contrast, there were no detectable effects on pheromone signaling caused by deletion or overexpression of YER158c, an open reading frame with overall sequence similarity to Afr1p that lacks this essential region. Interestingly, all of the AFR1 mutants showed a defect in their ability to form mating projections that was proportional to their defect in regulating pheromone signaling. This suggests that both functions may be due to the same action of Afr1p. Thus, these studies identify a specific region of Afr1p that is critical for its function in both signaling and morphogenesis.
Quantitative Trait Loci: A Meta-analysis
Authors: Goffinet Bruno , Gerber Sophie
Published: April 2021

This article presents a method to combine QTL results from different independent analyses. This method provides a modified Akaike criterion that can be used to decide how many QTL are actually represented by the QTL detected in different experiments. This criterion is computed to choose between models with one, two, three, etc., QTL. Simulations are carried out to investigate the quality of the model obtained with this method in various situations. It appears that the method allows the length of the confidence interval of QTL location to be consistently reduced when there are only very few “actual” QTL locations. An application of the method is given using data from the maize database available online at http://www.agron.missouri.edu/.
Quantitative Trait Loci Affecting Components of Wing Shape in Drosophila melanogaster
Authors: Zimmerman Erika , Palsson Arnar , Gibson Greg
Published: April 2021

Two composite multiple regression-interval mapping analyses were performed to identify candidate quantitative trait loci (QTL) affecting components of wing shape in Drosophila melanogaster defined by eight relative warp-based measures. A recombinant inbred line design was used to map QTL for the shape of two intervein regions in the anterior compartment of the wing, using a high resolution map of retrotransposon insertion sites between Oregon-R and Russian 2b. A total of 35 QTL representing up to 23 different loci were identified, many of which are located near components of the epidermal growth factor-Ras signal transduction pathway that regulates vein vs. intervein decision making and vein placement. Over one-half of the loci were detected in both sexes, and just under one-half were detected at two different growth temperatures. Different loci were found to affect aspects of shape in each intervein region, confirming that the shape of the whole wing should be regarded as a compound trait composed of several developmental units. In addition, a reciprocal backcross design was used to map QTL affecting shape in the posterior compartment of the wings of 831 flies, using a molecular map of 16 allele-specific oligohybridization single nucleotide polymorphism (SNP) markers between two divergent inbred lines. A total of 13 QTL were detected and shown to have generally additive effects on separable components of shape, in both sexes. By contrast, 8 QTL that affected wing size in these backcrosses were nearly dominant in their effects. The results confirm at the genetic level that wing shape is regulated independent of wing size and set up the hypothesis that wing shape is regulated in part through the regulation of the length and positioning of wing veins, involving quantitative regulation of the activity of secreted growth factors.
A Gain-of-Function Screen for Genes That Affect the Development of the Drosophila Adult External Sensory Organ
Authors: Abdelilah-Seyfried Salim , Chan Yee-Ming , Zeng Chaoyang , Justice Nicholas J , Younger-Shepherd Susan , Sharp Linda E , Barbel Sandra , Meadows Sarah A , Jan Lily Yeh , Jan Yuh Nung
Published: April 2021

The Drosophila adult external sensory organ, comprising a neuron and its support cells, is derived from a single precursor cell via several asymmetric cell divisions. To identify molecules involved in sensory organ development, we conducted a tissue-specific gain-of-function screen. We screened 2293 independent P-element lines established by P. Rørth and identified 105 lines, carrying insertions at 78 distinct loci, that produced misexpression phenotypes with changes in number, fate, or morphology of cells of the adult external sensory organ. On the basis of the gain-of-function phenotypes of both internal and external support cells, we subdivided the candidate lines into three classes. The first class (52 lines, 40 loci) exhibits partial or complete loss of adult external sensory organs. The second class (38 lines, 28 loci) is associated with increased numbers of entire adult external sensory organs or subsets of sensory organ cells. The third class (15 lines, 10 loci) results in potential cell fate transformations. Genetic and molecular characterization of these candidate lines reveals that some loci identified in this screen correspond to genes known to function in the formation of the peripheral nervous system, such as big brain, extra macrochaetae, and numb. Also emerging from the screen are a large group of previously uncharacterized genes and several known genes that have not yet been implicated in the development of the peripheral nervous system.
Nucleotide Variation at the CHALCONE ISOMERASE Locus in Arabidopsis thaliana
Authors: Kuittinen Helmi , Aguadé Montserrat
Published: April 2021

An ~1.9-kb region encompassing the CHI gene, which encodes chalcone isomerase, was sequenced in 24 worldwide ecotypes of Arabidopsis thaliana (L.) Heynh. and in 1 ecotype of A. lyrata ssp. petraea. There was no evidence for dimorphism at the CHI region. A minimum of three recombination events was inferred in the history of the sampled ecotypes of the highly selfing A. thaliana. The estimated nucleotide diversity (θTOTAL = 0.004, θSIL = 0.005) was on the lower part of the range of the corresponding estimates for other gene regions. The skewness of the frequency spectrum toward an excess of low-frequency polymorphisms, together with the bell-shaped distribution of pairwise nucleotide differences at CHI, suggests that A. thaliana has recently experienced a rapid population growth. Although this pattern could also be explained by a recent selective sweep at the studied region, results from the other studied loci and from an AFLP survey seem to support the expansion hypothesis. Comparison of silent polymorphism and divergence at the CHI region and at the Adh1 and ChiA revealed in some cases a significant deviation of the direct relationship predicted by the neutral theory, which would be compatible with balancing selection acting at the latter regions.
Genetic Drift in an Infinite Population: The Pseudohitchhiking Model
Authors: Gillespie John H
Published: April 2021

Selected substitutions at one locus can induce stochastic dynamics that resemble genetic drift at a closely linked neutral locus. The pseudohitchhiking model is a one-locus model that approximates these effects and can be used to describe the major consequences of linked selection. As the changes in neutral allele frequencies when hitchhiking are rapid, diffusion theory is not appropriate for studying neutral dynamics. A stationary distribution and some results on substitution processes are presented that use the theory of continuous-time Markov processes with discontinuous sample paths. The coalescent of the pseudohitchhiking model is shown to have a random number of branches at each node, which leads to a frequency spectrum that is different from that of the equilibrium neutral model. If genetic draft, the name given to these induced stochastic effects, is a more important stochastic force than genetic drift, then a number of paradoxes that have plagued population genetics disappear.
A Glucose Transporter Chimera Confers a Dominant Negative Glucose Starvation Phenotype in Saccharomyces cerevisiae
Authors: Sherwood Peter W , Katic Iskra , Sanz Pascual , Carlson Marian
Published: April 2021

A family of glucose transporters mediates glucose uptake in Saccharomyces cerevisiae. We show that the dominant mutation GSF4-1, which impairs glucose repression of SUC2, results in a nonfunctional chimera of the transporters Hxt1p and Hxt4p. Hxt1/4p inhibits the function of wild-type glucose transporters. Similar mutations may facilitate analysis of the major facilitator superfamily.
Sex Determination in the Drosophila Germline Is Dictated by the Sexual Identity of the Surrounding Soma
Authors: Waterbury J A , Horabin J I , Bopp D , Schedl P
Published: April 2021

It has been suggested that sexual identity in the germline depends upon the combination of a nonautonomous somatic signaling pathway and an autonomous X chromosome counting system. In the studies reported here, we have examined the role of the sexual differentiation genes transformer (tra) and doublesex (dsx) in regulating the activity of the somatic signaling pathway. We asked whether ectopic somatic expression of the female products of the tra and dsx genes could feminize the germline of XY animals. We find that TraF is sufficient to feminize XY germ cells, shutting off the expression of male-specific markers and activating the expression of female-specific markers. Feminization of the germline depends upon the constitutively expressed transformer-2 (tra-2) gene, but does not seem to require a functional dsx gene. However, feminization of XY germ cells by TraF can be blocked by the male form of the Dsx protein (DsxM). Expression of the female form of dsx, DsxF, in XY animals also induced germline expression of female markers. Taken together with a previous analysis of the effects of mutations in tra, tra-2, and dsx on the feminization of XX germ cells in XX animals, our findings indicate that the somatic signaling pathway is redundant at the level tra and dsx. Finally, our studies call into question the idea that a cell-autonomous X chromosome counting system plays a central role in germline sex determination.
When Did the Human Population Size Start Increasing?
Authors: Wall Jeffrey D , Przeworski Molly
Published: April 2021

We analyze the frequency spectra of all available human nuclear sequence data sets by using a model of constant population size followed by exponential growth. Parameters of growth (more extreme than or) comparable to what has been suggested from mtDNA data can be rejected for 6 out of the 10 largest data sets. When the data are separated into African and non-African samples, a constant size no-growth model can be rejected for 4 out of 8 non-African samples. Long-term growth (i.e., starting 50–100 kya) can be rejected for 2 out of 8 African samples and 5 out of 8 non-African ones. Under more complex demographic models, including a bottleneck or population subdivision, more of the data are compatible with long-term growth. One problem with the data used here is that a subset of loci may reflect the action of natural selection as well as of demography. It remains possible that the correct demographic model is one of constant population size followed by long-term growth but that at several loci the demographic signature has been obscured by balancing or diversifying selection. However, it is not clear that the data at these loci are consistent with a simple model of balancing selection; more complicated selective alternatives cannot be tested unless they are made explicit. An alternative explanation is that population size growth is more recent (e.g., upper Paleolithic) and that some of the loci have experienced recent directional selection. Given the available data, the latter hypothesis seems more likely.
Deletion of a Conserved Regulatory Element in the Drosophila Adh Gene Leads to Increased Alcohol Dehydrogenase Activity but Also Delays Development
Authors: Parsch John , Russell Jacob A , Beerman Isabel , Hartl Daniel L , Stephan Wolfgang
Published: April 2021

In vivo levels of enzymatic activity may be increased through either structural or regulatory changes. Here we use Drosophila melanogaster alcohol dehydrogenase (ADH) in an experimental test for selective differences between these two mechanisms. The well-known ADH-Slow (S)/Fast (F) amino acid replacement leads to a twofold increase in activity by increasing the catalytic efficiency of the enzyme. Disruption of a highly conserved, negative regulatory element in the Adh 3′ UTR also leads to a twofold increase in activity, although this is achieved by increasing in vivo Adh mRNA and protein concentrations. These two changes appear to be under different types of selection, with positive selection favoring the amino acid replacement and purifying selection maintaining the 3′ UTR sequence. Using transgenic experiments we show that deletion of the conserved 3′ UTR element increases adult and larval Adh expression in both the ADH-F and ADH-S genetic backgrounds. However, the 3′ UTR deletion also leads to a significant increase in developmental time in both backgrounds. ADH allozyme type has no detectable effect on development. These results demonstrate a negative fitness effect associated with Adh overexpression. This provides a mechanism whereby natural selection can discriminate between alternative pathways of increasing enzymatic activity.
Identification and Characterization of TUP1-Regulated Genes in Candida albicans
Authors: Braun Burkhard R , Head W Steven , Wang Ming X , Johnson Alexander D
Published: April 2021

TUP1 encodes a transcriptional repressor that negatively controls filamentous growth in Candida albicans. Using subtractive hybridization, we identified six genes, termed repressed by TUP1 (RBT), whose expression is regulated by TUP1. One of the genes (HWP1) has previously been characterized, and a seventh TUP1-repressed gene (WAP1) was recovered due to its high similarity to RBT5. These genes all encode secreted or cell surface proteins, and four out of the seven (HWP1, RBT1, RBT5, and WAP1) encode putatively GPI-modified cell wall proteins. The remaining three, RBT2, RBT4, and RBT7, encode, respectively, an apparent ferric reductase, a plant pathogenesis-related protein (PR-1), and a putative secreted RNase T2. The expression of RBT1, RBT4, RBT5, HWP1, and WAP1 was induced in wild-type cells during the switch from the yeast form to filamentous growth, indicating the importance of TUP1 in regulating this process and implicating the RBTs in hyphal-specific functions. We produced knockout strains in C. albicans for RBT1, RBT2, RBT4, RBT5, and WAP1 and detected no phenotypes on several laboratory media. However, two animal models for C. albicans infection, a rabbit cornea model and a mouse systemic infection model, revealed that rbt1Δ and rbt4Δ strains had significantly reduced virulence. TUP1 appears, therefore, to regulate many genes in C. albicans, a significant fraction of which are induced during filamentous growth, and some of which participate in pathogenesis.
Production and Characterization of Maize Chromosome 9 Radiation Hybrids Derived From an Oat-Maize Addition Line
Authors: Riera-Lizarazu O , Vales M I , Ananiev E V , Rines H W , Phillips R L
Published: April 2021

In maize (Zea mays L., 2n = 2x = 20), map-based cloning and genome organization studies are often complicated because of the complexity of the genome. Maize chromosome addition lines of hexaploid cultivated oat (Avena sativa L., 2n = 6x = 42), where maize chromosomes can be individually manipulated, represent unique materials for maize genome analysis. Maize chromosome addition lines are particularly suitable for the dissection of a single maize chromosome using radiation because cultivated oat is an allohexaploid in which multiple copies of the oat basic genome provide buffering to chromosomal aberrations and other mutations. Irradiation (gamma rays at 30, 40, and 50 krad) of a monosomic maize chromosome 9 addition line produced maize chromosome 9 radiation hybrids (M9RHs)—oat lines possessing different fragments of maize chromosome 9 including intergenomic translocations and modified maize addition chromosomes with internal and terminal deletions. M9RHs with 1 to 10 radiation-induced breaks per chromosome were identified. We estimated that a panel of 100 informative M9RHs (with an average of 3 breaks per chromosome) would allow mapping at the 0.5- to 1.0-Mb level of resolution. Because mapping with maize chromosome addition lines and radiation hybrid derivatives involves assays for the presence or absence of a given marker, monomorphic markers can be quickly and efficiently mapped to a chromosome region. Radiation hybrid derivatives also represent sources of region-specific DNA for cloning of genes or DNA markers.
The Cofactor-Dependent Pathways for α- and β-Tubulins in Microtubule Biogenesis Are Functionally Different in Fission Yeast
Authors: Radcliffe Pippa A , Garcia Miguel Angel , Toda Takashi
Published: April 2021

The biogenesis of microtubules in the cell comprises a series of complex steps, including protein-folding reactions catalyzed by chaperonins. In addition a group of evolutionarily conserved proteins, called cofactors (A to E), is required for the production of assembly-competent α-/β-tubulin heterodimers. Using fission yeast, in which alp11+, alp1+, and alp21+, encoding the homologs for cofactors B, D, and E, respectively, are essential for cell viability, we have undertaken the genetic analysis of alp31+, the homolog of cofactor A. Gene disruption analysis shows that, unlike the three genes mentioned above, alp31+ is dispensable for cell growth and division. Nonetheless, detailed analysis of alp31-deleted cells demonstrates that Alp31A is required for the maintenance of microtubule structures and, consequently, the proper control of growth polarity. alp31-deleted cells show genetic interactions with mutations in β-tubulin, but not in α-tubulin. Budding yeast cofactor A homolog RBL2 is capable of suppressing the polarity defects of alp31-deleted cells. We conclude that the cofactor-dependent biogenesis of microtubules comprises an essential and a nonessential pathway, both of which are required for microtubule integrity.
A Role for Cytosolic Hsp70 in Yeast [PSI+] Prion Propagation and [PSI+] as a Cellular Stress
Authors: Jung Giman , Jones Gary , Wegrzyn Renee D , Masison Daniel C
Published: April 2021

[PSI+] is a prion (infectious protein) of Sup35p, a subunit of the Saccharomyces cerevisiae translation termination factor. We isolated a dominant allele, SSA1-21, of a gene encoding an Hsp70 chaperone that impairs [PSI+] mitotic stability and weakens allosuppression caused by [PSI+]. While [PSI+] stability is normal in strains lacking SSA1, SSA2, or both, SSA1-21 strains with a deletion of SSA2 cannot propagate [PSI+]. SSA1-21 [PSI+] strains are hypersensitive to curing of [PSI+] by guanidine-hydrochloride and partially cured of [PSI+] by rapid induction of the heat-shock response but not by growth at 37°. The number of inheritable [PSI+] particles is significantly reduced in SSA1-21 cells. SSA1-21 effects on [PSI+] appear to be independent of Hsp104, another stress-inducible protein chaperone known to be involved in [PSI+] propagation. We propose that cytosolic Hsp70 is important for the formation of Sup35p polymers characteristic of [PSI+] from preexisting material and that Ssa1-21p both lacks and interferes with this activity. We further demonstrate that the negative effect of heat stress on [PSI+] phenotype directly correlates with solubility of Sup35p and find that in wild-type strains the presence of [PSI+] causes a stress that elevates basal expression of Hsp104 and SSA1.
Isolation and Analysis of Six timeless Alleles That Cause Short- or Long-Period Circadian Rhythms in Drosophila
Authors: Rothenfluh Adrian , Abodeely Marla , Price Jeffrey L , Young Michael W
Published: April 2021

In genetic screens for Drosophila mutations affecting circadian locomotion rhythms, we have isolated six new alleles of the timeless (tim) gene. Two of these mutations cause short-period rhythms of 21–22 hr in constant darkness, and four result in long-period cycles of 26–28 hr. All alleles are semidominant. Studies of the genetic interactions of some of the tim alleles with period-altering period (per) mutations indicate that these interactions are close to multiplicative; a given allele changes the period length of the genetic background by a fixed percentage, rather than by a fixed number of hours. The timL1 allele was studied in molecular detail. The long behavioral period of timL1 is reflected in a lengthened molecular oscillation of per and tim RNA and protein levels. The lengthened period is partly caused by delayed nuclear translocation of TIML1 protein, shown directly by immunocytochemistry and indirectly by an analysis of the phase response curve of timL1 flies.
Computational and Experimental Characterization of Physically Clustered Simple Sequence Repeats in Plants
Authors: Cardle Linda , Ramsay Luke , Milbourne Dan , Macaulay Malcolm , Marshall David , Waugh Robbie
Published: April 2021

The type and frequency of simple sequence repeats (SSRs) in plant genomes was investigated using the expanding quantity of DNA sequence data deposited in public databases. In Arabidopsis, 306 genomic DNA sequences longer than 10 kb and 36,199 EST sequences were searched for all possible mono- to pentanucleotide repeats. The average frequency of SSRs was one every 6.04 kb in genomic DNA, decreasing to one every 14 kb in ESTs. SSR frequency and type differed between coding, intronic, and intergenic DNA. Similar frequencies were found in other plant species. On the basis of these findings, an approach is proposed and demonstrated for the targeted isolation of single or multiple, physically clustered SSRs linked to any gene that has been mapped using low-copy DNA-based markers. The approach involves sample sequencing a small number of subclones of selected randomly sheared large insert DNA clones (e.g., BACs). It is shown to be both feasible and practicable, given the probability of fortuitously sequencing through an SSR. The approach is demonstrated in barley where sample sequencing 34 subclones of a single BAC selected by hybridization to the Big1 gene revealed three SSRs. These allowed Big1 to be located at the top of barley linkage group 6HS.
The necrotic Gene in Drosophila Corresponds to One of a Cluster of Three Serpin Transcripts Mapping at 43A1.2
Authors: Green Clare , Levashina Elena , McKimmie Carol , Dafforn Tim , Reichhart Jean-Marc , Gubb David
Published: April 2021

Mutants of the necrotic (nec) gene in Drosophila melanogaster die in the late pupal stage as pharate adults, or hatch as weak, but relatively normal-looking, flies. Adults develop black melanized spots on the body and leg joints, the abdomen swells with hemolymph, and flies die within 3 or 4 days of eclosion. The TOLL-mediated immune response to fungal infections is constitutively activated in nec mutants and pleiotropic phenotypes include melanization and cellular necrosis. These changes are consistent with activation of one or more proteolytic cascades. The nec gene corresponds to Spn43Ac, one of a cluster of three putative serine proteinase inhibitors at 43A1.2, on the right arm of chromosome 2. Although serpins have been implicated in the activation of many diverse pathways, lack of an individual serpin rarely causes a detectable phenotype. Absence of Spn43Ac, however, gives a clear phenotype, which will allow a mutational analysis of critical features of the molecular structure of serpins.
Genetic Basis of Climatic Adaptation in Scots Pine by Bayesian Quantitative Trait Locus Analysis
Authors: Hurme Päivi , Sillanpää Mikko J , Arjas Elja , Repo Tapani , Savolainen Outi
Published: April 2021

We examined the genetic basis of large adaptive differences in timing of bud set and frost hardiness between natural populations of Scots pine. As a mapping population, we considered an “open-pollinated backcross” progeny by collecting seeds of a single F1 tree (cross between trees from southern and northern Finland) growing in southern Finland. Due to the special features of the design (no marker information available on grandparents or the father), we applied a Bayesian quantitative trait locus (QTL) mapping method developed previously for outcrossed offspring. We found four potential QTL for timing of bud set and seven for frost hardiness. Bayesian analyses detected more QTL than ANOVA for frost hardiness, but the opposite was true for bud set. These QTL included alleles with rather large effects, and additionally smaller QTL were supported. The largest QTL for bud set date accounted for about a fourth of the mean difference between populations. Thus, natural selection during adaptation has resulted in selection of at least some alleles of rather large effect.