bluuebunny/crossref_metadata_2025 huggingface dataset:
Nonparametric Disequilibrium Mapping of Functional Sites Using Haplotypes of Multiple Tightly Linked Single-Nucleotide Polymorphism Markers
Authors: Cheng Rong , Ma Jennie Z , Wright Fred A , Lin Shili , Gao Xin , Wang Daolong , Elston Robert C , Li Ming D
Published: April 2021

As the speed and efficiency of genotyping single-nucleotide polymorphisms (SNPs) increase, using the SNP map, it becomes possible to evaluate the extent to which a common haplotype contributes to the risk of disease. In this study we propose a new procedure for mapping functional sites or regions of a candidate gene of interest using multiple linked SNPs. Based on a case-parent trio family design, we use expectation-maximization (EM) algorithm-derived haplotype frequency estimates of multiple tightly linked SNPs from both unambiguous and ambiguous families to construct a contingency statistic S for linkage disequilibrium (LD) analysis. In the procedure, a moving-window scan for functional SNP sites or regions can cover an unlimited number of loci except for the limitation of computer storage. Within a window, all possible widths of haplotypes are utilized to find the maximum statistic S* for each site (or locus). Furthermore, this method can be applied to regional or genome-wide scanning for determining linkage disequilibrium using SNPs. The sensitivity of the proposed procedure was examined on the simulated data set from the Genetic Analysis Workshop (GAW) 12. Compared with the conventional and generalized TDT methods, our procedure is more flexible and powerful.
On the Genomic Location of theexuperantia1Gene inDrosophila miranda: The Limits ofin SituHybridization Experiments
Authors: Bachtrog Doris , Charlesworth Brian
Published: April 2021

In situ hybridization to Drosophila polytene chromosomes is a powerful tool for determining the chromosomal location of genes. Using in situ hybridization experiments, Yi and Charlesworth recently reported the transposition of the exuperantia1 gene (exu1) from a neo-sex chromosome to the ancestral X chromosome of Drosophila miranda, close to exuperantia2 (exu2). By characterizing sequences flanking exu1, however, we found the position of exu1 to be conserved on the neo-sex chromosome. Further, the exu2 gene was found to be tandemly duplicated on the X chromosome of D. miranda. The misleading hybridization signal of exu1 may be caused by multiple copies of exu2, which interfere with the hybridization of the exu1 probe to its genomic position on the neo-X chromosome. This suggests that flanking DNA should be used to confirm the positions of members of gene families.
Using Evolutionary Rates to Investigate Protein Functional Divergence and Conservation: A Case Study of the Carbonic Anhydrases
Authors: Knudsen Bjarne , Miyamoto Michael M , Laipis Philip J , Silverman David N
Published: April 2021

Functional constraints on proteins limit their evolutionary rates at specific sites. These constraints allow for the interpretation of conserved residues and sites with a rate change as those most likely underlying the functional similarities and differences among protein subfamilies, respectively. This study describes new likelihood-ratio tests (LRTs) that complement existing ones for the identification of both conserved and rate change sites. These identifications are validated by the recovery of residues that are known from existing biochemical and structural information to be critical for the functional similarities and differences among carbonic anhydrases (CAs). In combination with this other information, these LRTs also support a unique antioxidant defense role for the puzzling CA III. As illustrated by the CAs, these LRTs, in combination with other biological evidence, offer a powerful and cost-effective approach for testing hypotheses, making predictions, and designing experiments in protein functional studies.
Translational Selection and Yeast Proteome Evolution
Authors: Akashi Hiroshi
Published: April 2021

The primary structures of peptides may be adapted for efficient synthesis as well as proper function. Here, the Saccharomyces cerevisiae genome sequence, DNA microarray expression data, tRNA gene numbers, and functional categorizations of proteins are employed to determine whether the amino acid composition of peptides reflects natural selection to optimize the speed and accuracy of translation. Strong relationships between synonymous codon usage bias and estimates of transcript abundance suggest that DNA array data serve as adequate predictors of translation rates. Amino acid usage also shows striking relationships with expression levels. Stronger correlations between tRNA concentrations and amino acid abundances among highly expressed proteins than among less abundant proteins support adaptation of both tRNA abundances and amino acid usage to enhance the speed and accuracy of protein synthesis. Natural selection for efficient synthesis appears to also favor shorter proteins as a function of their expression levels. Comparisons restricted to proteins within functional classes are employed to control for differences in amino acid composition and protein size that reflect differences in the functional requirements of proteins expressed at different levels.
Depletion of H2A-H2B Dimers in Saccharomyces cerevisiae Triggers Meiotic Arrest by Reducing IME1 Expression and Activating the BUB2-Dependen Branch of the Spindle Checkpoint
Authors: Hanlon Sean E , Norris David N , Vershon Andrew K
Published: April 2021

In the yeast Saccharomyces cerevisiae, diploid strains carrying homozygous hta1-htb1Δ mutations express histone H2A-H2B dimers at a lower level than do wild-type cells. Although this mutation has only minor effects on mitotic growth, it causes an arrest in sporulation prior to the first meiotic division. In this report, we show that the hta1-htb1Δ mutant exhibits reduced expression of early and middle-sporulation-specific genes and that the meiotic arrest of the hta1-htb1Δ mutant can be partially bypassed by overexpression of IME1. Additionally, deletions of BUB2 or BFA1, components of one branch of the spindle checkpoint pathway, bypass the meiotic arrest. Mutations in the other branch of the pathway or in the pachytene checkpoint are unable to suppress the meiotic block. These observations indicate that depletion of the H2A-H2B dimer blocks sporulation by at least two mechanisms: disruption of the expression of meiotic regulatory genes and activation of the spindle checkpoint. Our results show that the failure to progress through the meiotic pathway is not the result of global chromosomal alterations but that specific aspects of meiosis are sensitive to depletion of the H2A-H2B dimer.
Inferences on the Evolutionary History of theDrosophila americanaPolymorphicX/4Fusion From Patterns of Polymorphism at theX-LinkedparalyticandelavGenes
Authors: Vieira Cristina P , Coelho Paula A , Vieira Jorge
Published: April 2021

In Drosophila there is limited evidence on the nature of evolutionary forces affecting chromosomal arrangements other than inversions. The study of the X/4 fusion polymorphism of Drosophila americana is thus of interest. Polymorphism patterns at the paralytic (para) gene, located at the base of the X chromosome, suggest that there is suppressed crossing over in this region between fusion and nonfusion chromosomes but not within fusion and nonfusion chromosomes. These data are thus compatible with previous claims that within fusion chromosomes the amino acid clines found at fused1 (also located at the base of the X chromosome) are likely maintained by local selection. The para data set also suggests a young age of the X/4 fusion. Polymorphism data on para and elav (located at the middle region of the X chromosome) suggest that there is no population structure other than that caused by the X/4 fusion itself. These findings are therefore compatible with previous claims that selection maintains the strong association observed between the methionine/threonine variants at fused1 and the status of the X chromosome as fused or unfused to the fourth chromosome.
Human Population Structure and Its Effects on Sampling Y Chromosome Sequence Variation
Authors: Hammer Michael F , Blackmer Felisa , Garrigan Dan , Nachman Michael W , Wilder Jason A
Published: April 2021

The excess of rare variants in global sequencing studies of the nonrecombining portion of the Y chromosome (NRY) has been interpreted as evidence for the effects of human demographic expansion. However, many NRY polymorphisms are geographically localized and the effect of different geographical sampling on patterns of NRY variation is unknown. We use two sampling designs to detect population structure and its effects on patterns of human NRY polymorphism. First, we sequence 26.5 kb of noncoding Y chromosome DNA from 92 globally distributed males representing 35 populations. We find that the number of polymorphisms with singleton variants is positively correlated with the number of populations sampled and that there is a significant negative correlation of Tajima’s D (TD) and Fu and Li’s D (FD) statistics with the number of pooled populations. We then sequence the same region in a total of 73 males sampled from 3 distinct populations and find that TD and FD values for the 3 pooled and individual population samples were much less negative than those in the aforementioned global sample. Coalescent simulations show that a simple splitting model of population structure, with no changes in population size, is sufficient to produce the negative values of TD seen in our pooled samples. These empirical and simulation results suggest that observed levels of NRY population structure may lead to an upward bias in the number of singleton variants in global surveys and call into question inferences of population expansion based on global sampling strategies.
Pedigree Data Analysis With Crossover Interference
Authors: Browning Sharon
Published: April 2021

We propose a new method for calculating probabilities for pedigree genetic data that incorporates crossover interference using the chi-square models. Applications include relationship inference, genetic map construction, and linkage analysis. The method is based on importance sampling of unobserved inheritance patterns conditional on the observed genotype data and takes advantage of fast algorithms for no-interference models while using reweighting to allow for interference. We show that the method is effective for arbitrarily many markers with small pedigrees.
Dimension Reduction for Mapping mRNA Abundance as Quantitative Traits
Authors: Lan Hong , Stoehr Jonathan P , Nadler Samuel T , Schueler Kathryn L , Yandell Brian S , Attie Alan D
Published: April 2021

The advent of sophisticated genomic techniques for gene mapping and microarray analysis has provided opportunities to map mRNA abundance to quantitative trait loci (QTL) throughout the genome. Unfortunately, simple mapping of each individual mRNA trait on the scale of a typical microarray experiment is computationally intensive, subject to high sample variance, and therefore underpowered. However, this problem can be addressed by capitalizing on correlation among the large number of mRNA traits. We present a method to reduce the dimensionality for mapping gene expression data as quantitative traits. We used a blind method, principal components, and a sighted method, hierarchical clustering seeded by disease relevant traits, to define new traits composed of a small collection of promising mRNAs. We validated the principle of our approach by mapping the expression levels of metabolism genes in a population of F2-ob/ob mice derived from the BTBR and C57BL/6J strains. We found that lipogenic and gluconeogenic mRNAs, which are known targets of insulin action, were closely associated with the insulin trait. Multiple interval mapping and Bayesian interval mapping of this new trait revealed significant linkages to chromosome regions that were contained in loci associated with type 2 diabetes in this same mouse sample. As a further statistical refinement, we show that principal component analysis also effectively reduced dimensions for mapping phenotypes composed of mRNA abundances.
The Anomalous Effects of Biased Mutation
Authors: Waxman D , Peck J R
Published: April 2021

A model is presented in which alleles at a number of loci combine to influence the value of a quantitative trait that is subject to stabilizing selection. Mutations can occur to alleles at the loci under consideration. Some of these mutations will tend to increase the value of the trait, while others will tend to decrease it. In contrast to most previous models, we allow the mean effect of mutations to be nonzero. This means that, on average, mutations can have a bias, such that they tend to either increase or decrease the value of the trait. We find, unsurprisingly, that biased mutation moves the equilibrium mean value of the quantitative trait in the direction of the bias. What is more surprising is the behavior of the deviation of the equilibrium mean value of the trait from its optimal value. This has a nonmonotonic dependence on the degree of bias, so that increasing the degree of bias can actually bring the mean phenotype closer to the optimal phenotype. Furthermore, there is a definite maximum to the extent to which biased mutation can cause a difference between the mean phenotype and the optimum. For plausible parameter values, this maximum-possible difference is small. Typically, quantitative-genetics models assume an unconstrained model of mutation, where the expected difference in effect between a parental allele and a mutant allele is independent of the current state of the parental allele. Our results show that models of this sort can easily lead to biologically implausible consequences when mutations are biased. In particular, unconstrained mutation typically leads to a continual increase or decrease in the mean allelic effects at all trait-controlling loci. Thus at each of these loci, the mean allelic effect eventually becomes extreme. This suggests that some of the models of mutation most commonly used in quantitative genetics should be modified so as to introduce genetic constraints.
The Effect of Neutral Nonadditive Gene Action on the Quantitative Index of Population Divergence
Authors: López-Fanjul Carlos , Fernández Almudena , Toro Miguel A
Published: April 2021

For neutral additive genes, the quantitative index of population divergence (QST) is equivalent to Wright’s fixation index (FST). Thus, divergent or convergent selection is usually invoked, respectively, as a cause of the observed increase (QST > FST) or decrease (QST < FST) of QST from its neutral expectation (QST = FST). However, neutral nonadditive gene action can mimic the additive expectations under selection. We have studied theoretically the effect of consecutive population bottlenecks on the difference FST - QST for two neutral biallelic epistatic loci, covering all types of marginal gene action. With simple dominance, QST < FST for only low to moderate frequencies of the recessive alleles; otherwise, QST > FST. Additional epistasis extends the condition QST < FST to a broader range of frequencies. Irrespective of the type of nonadditive action, QST < FST generally implies an increase of both the within-line additive variance after bottlenecks over its ancestral value (VA) and the between-line variance over its additive expectation (2FSTVA). Thus, both the redistribution of the genetic variance after bottlenecks and the FST - QST value are governed largely by the marginal properties of single loci. The results indicate that the use of the FST - QST criterion to investigate the relative importance of drift and selection in population differentiation should be restricted to pure additive traits.
Genetics of cosQ, the DNA-Packaging Termination Site of Phage λ: Local Suppressors and Methylation Effects
Authors: Wieczorek Douglas J , Feiss Michael
Published: April 2021

The cos site of the bacteriophage λ chromosome contains the sites required for DNA processing and packaging during virion assembly. cos is composed of three subsites, cosQ, cosN, and cosB. cosQ is required for the termination of chromosome packaging. Previous studies have shown cosQ mutations to be suppressed in three ways: by a local suppressor within cosQ; by an increase in the length of the λ chromosome; and by missense mutations affecting the prohead's portal protein, gpB. In the first study reported here, revertants of a set of cosQ mutants were screened for suppressors, and cis-acting suppressors of cosQ mutations were studied; these included second-site cosQ point mutations, base-pair insertions within cosQ, and an additional genome-lengthening suppressor. The 7-bp-long cosQ, with the sequence 5′-GGGTCCT-3′, coincides exactly with the recognition site for the EcoO109I restriction/methylation system, which has the consensus sequence 5′-PuGGNCCPy-3′. In a second study, EcoO109I methylation was found to strongly interfere with the residual cosQ function of leaky cosQ mutants. cis-acting suppressors that overcome methylation-associated defects, including a methylation-dependent suppressor, were also isolated. Models of cosQ suppression are presented.
Rare Deep-Rooting Y Chromosome Lineages in Humans: Lessons for Phylogeography
Authors: Weale Michael E , Shah Tina , Jones Abigail L , Greenhalgh John , Wilson James F , Nymadawa Pagbajabyn , Zeitlin David , Connell Bruce A , Bradman Neil , Thomas Mark G
Published: April 2021

There has been considerable debate on the geographic origin of the human Y chromosome Alu polymorphism (YAP). Here we report a new, very rare deep-rooting haplogroup within the YAP clade, together with data on other deep-rooting YAP clades. The new haplogroup, found so far in only five Nigerians, is the least-derived YAP haplogroup according to currently known binary markers. However, because the interior branching order of the Y chromosome genealogical tree remains unknown, it is impossible to impute the origin of the YAP clade with certainty. We discuss the problems presented by rare deep-rooting lineages for Y chromosome phylogeography.
Human Handedness and Scalp Hair-Whorl Direction Develop From a Common Genetic Mechanism
Authors: Klar Amar J S
Published: April 2021

Theories concerning the cause of right- or left-hand preference in humans vary from purely learned behavior, to solely genetics, to a combination of the two mechanisms. The cause of handedness and its relation to the biologically specified scalp hair-whorl rotation is determined here. The general public, consisting of mostly right-handers (RH), shows counterclockwise whorl rotation infrequently in 8.4% of individuals. Interestingly, non-right-handers (NRH, i.e., left-handers and ambidextrous) display a random mixture of clockwise and counterclockwise swirling patterns. Confirming this finding, in another independent sample of individuals chosen because of their counterclockwise rotation, one-half of them are NRH. These findings of coupling in RH and uncoupling in NRH unequivocally establish that these traits develop from a common genetic mechanism. Another result concerning handedness of the progeny of discordant monozygotic twins suggests that lefties are one gene apart from righties. Together, these results suggest (1) that a single gene controls handedness, whorl orientation, and twin concordance and discordance and (2) that neuronal and visceral (internal organs) forms of bilateral asymmetry are coded by separate sets of genetic pathways. The sociological impact of the study is discussed.
Haplotype Sharing Refines the Location of an Imprinted Quantitative Trait Locus With Major Effect on Muscle Mass to a 250-kb Chromosome Segment Containing the Porcine IGF2 Gene
Authors: Nezer Carine , Collette Catherine , Moreau Laurence , Brouwers Benoît , Kim Jong-Joo , Giuffra Elisabetta , Buys Nadine , Andersson Leif , Georges Michel
Published: April 2021

We herein describe the fine mapping of an imprinted QTL with major effect on muscle mass that was previously assigned to distal SSC2p in the pig. The proposed approach exploits linkage disequilibrium in combination with QTL genotyping by marker-assisted segregation analysis. By identifying a haplotype shared by all “Q” chromosomes, we map the QTL to an ∼250-kb chromosome segment containing INS and IGF2 as the only known paternally expressed genes. This considerably reinforces the candidacy of these genes, justifying their detailed analysis.
Undulated short-tailDeletion Mutation in the Mouse AblatesPax1and Leads to Ectopic Activation of NeighboringNkx2-2in Domains That Normally ExpressPax1
Authors: Kokubu Chikara , Wilm Bettina , Kokubu Tomoko , Wahl Matthias , Rodrigo Isabel , Sakai Norio , Santagati Fabio , Hayashizaki Yoshihide , Suzuki Misao , Yamamura Ken-ichi , Abe Kuniya , Imai Kenji
Published: April 2021

Previous studies have indicated that the Undulated short-tail deletion mutation in mouse Pax1 (Pax1Un-s) not only ablates Pax1, but also disturbs a gene or genes nearby Pax1. However, which gene(s) is involved and how the Pax1Un-s phenotype is confined to the Pax1-positive tissues remain unknown. In the present study, we determined the Pax1Un-s deletion interval to be 125 kb and characterized genes around Pax1. We show that the Pax1Un-s mutation affects four physically linked genes within or near the deletion, including Pax1, Nkx2-2, and their potential antisense genes. Remarkably, Nkx2-2 is ectopically activated in the sclerotome and limb buds of Pax1Un-s embryos, both of which normally express Pax1. This result suggests that the Pax1Un-s deletion leads to an illegitimate interaction between remotely located Pax1 enhancers and the Nkx2-2 promoter by disrupting an insulation mechanism between Pax1 and Nkx2-2. Furthermore, we show that expression of Bapx1, a downstream target of Pax1, is more strongly affected in Pax1Un-s mutants than in Pax1-null mutants, suggesting that the ectopic expression of Nkx2-2 interferes with the Pax1-Bapx1 pathway. Taken together, we propose that a combination of a loss-of-function mutation of Pax1 and a gain-of-function mutation of Nkx2-2 is the molecular basis of the Pax1Un-s mutation.
Assessing Probability of Ancestry Using Simple Sequence Repeat Profiles: Applications to Maize Inbred Lines and Soybean Varieties
Authors: Berry Donald A , Seltzer Jon D , Xie Chongqing , Wright Deanne L , Jones Elizabeth S , Sebastian Scott , Smith J Stephen C
Published: April 2021

Determining parentage is a fundamental problem in biology and in applications such as identifying pedigrees. Difficulties inferring parentage derive from extensive inbreeding within the population, whether natural or planned; using an insufficient number of hypervariable loci; and from allele mismatches caused by mutation or by laboratory errors that generate false exclusions. Many studies of parentage have been limited to comparisons of small numbers of specific parent-progeny triplets. There have been few large-scale surveys of candidates in which there is no prior knowledge of parentage. We present an algorithm that determines the probability of parentage in circumstances where there is no prior knowledge of pedigree and that is robust in the face of missing data and mistyped data. The focus is parentage of an inbred line having uncertain ancestry. The algorithm is a variation of a previously published hybrid-focused algorithm. We describe the algorithm and demonstrate its performance in determining parentage of 43 inbred varieties of soybean that have been profiled using 236 SSR loci and from seven inbred varieties of maize that were profiled using 70 SSR loci. We include simulations of additional levels of missing and mistyped data to show the algorithm's utility and flexibility.
Patterns of Heteroduplex Formation Associated With the Initiation of Meiotic Recombination in the Yeast Saccharomyces cerevisiae
Authors: Merker Jason D , Dominska Margaret , Petes Thomas D
Published: April 2021

The double-strand break repair (DSBR) model of recombination predicts that heteroduplexes will be formed in regions that flank the double-strand break (DSB) site and that the resulting intermediate is resolved to generate either crossovers or noncrossovers for flanking markers. Previous studies in Saccharomyces cerevisiae, however, failed to detect heteroduplexes on both sides of the DSB site. Recent physical studies suggest that some recombination events involve heterodupex formation by a mechanism, synthesis-dependent strand annealing (SDSA), that is inherently asymmetric with respect to the DSB site and that leads exclusively to noncrossovers of flanking markers. Below, we demonstrate that many of the recombination events initiated at the HIS4 recombination hotspot are consistent with a variant of the DSBR model in which the extent of heteroduplex on one side of the DSB site is much greater than that on the other. Events that include only one flanking marker in the heteroduplex (unidirectional events) are usually resolved as noncrossovers, whereas events that include both flanking markers (bidirectional events) are usually resolved as crossovers. The unidirectional events may represent SDSA, consistent with the conclusions of others, although other possibilities are not excluded. We also show that the level of recombination reflects the integration of events initiated at several different DSB sites, and we identify a subset of gene conversion events that may involve break-induced replication (BIR) or repair of a double-stranded DNA gap.
Recombinogenic Effects of DNA-Damaging Agents Are Synergistically Increased by Transcription in Saccharomyces cerevisiae: New Insights Into Transcription-Associated Recombination
Authors: García-Rubio M , Huertas P , González-Barrera S , Aguilera A
Published: April 2021

Homologous recombination of a particular DNA sequence is strongly stimulated by transcription, a phenomenon observed from bacteria to mammals, which we refer to as transcription-associated recombination (TAR). TAR might be an accidental feature of DNA chemistry with important consequences for genetic stability. However, it is also essential for developmentally regulated processes such as class switching of immunoglobulin genes. Consequently, it is likely that TAR embraces more than one mechanism. In this study we tested the possibility that transcription induces recombination by making DNA more susceptible to recombinogenic DNA damage. Using different plasmid-chromosome and direct-repeat recombination constructs in which transcription is driven from either the PGAL1- or the Ptet-regulated promoters, we have

shown that either 4-nitroquinoline-N-oxide (4-NQO) or methyl methanesulfonate (MMS) produces a synergistic increase of recombination when combined with transcription. 4-NQO and MMS stimulated recombination of a transcriptionally active DNA sequence up to 12,800- and 130-fold above the spontaneous levels observed in the absence of transcription, whereas 4-NQO and MMS alone increased recombination 193- and 4.5-fold, respectively. Our results provide evidence that TAR is due, at least in part, to the ability of transcription to enhance the accessibility of DNA to exogenous chemicals and internal metabolites responsible for recombinogenic lesions. We discuss possible parallelisms between the mechanisms of induction of recombination and mutation by transcription.
The Aspergillus nidulans swoC1 Mutant Shows Defects in Growth and Development
Authors: Lin Xiaorong , Momany Michelle
Published: April 2021

Previous work identified swoC1 as a single-gene mutant with defects in polarity establishment. In this study swoC1 was shown to have defects in endocytosis, compartmentation, nuclear distribution, and conidiation. Temperature-shift experiments showed that the swoC1 mutant establishes multiple random sites of germ tube emergence. Surprisingly, these experiments also showed that even a slight delay in polarity establishment causes defects in later vegetative growth and asexual reproduction. The swoC gene was mapped to the centromere of chromosome III and cloned by complementation of the temperature-sensitive phenotype. The predicted SwoCp is homologous to rRNA pseudouridine synthases of yeast (Cbf5p) and humans (Dkc1p). However, neither rRNA pseudouridine synthesis nor rRNA processing appears to be affected in the swoC1 mutant. The swoC1 mutation occurs in the putative RNA-binding domain upstream of the C terminus, leaving the N-terminal TRUB catalytic domain intact. Interestingly, while deletion of the swoC gene was lethal in A. nidulans, the C terminus, including NLS, microtubule-binding, and coiled-coil domains, was dispensable for growth. SwoCp likely plays an important role in polar growth and nuclear distribution in A. nidulans, functions not yet described for its homologs.
Dominance and Overdominance of Mildly Deleterious Induced Mutations for Fitness Traits in Caenorhabditis elegans
Authors: Peters A D , Halligan D L , Whitlock M C , Keightley P D
Published: April 2021

We estimated the average dominance coefficient of mildly deleterious mutations (h, the proportion by which mutations in the heterozygous state reduce fitness components relative to those in the homozygous state) in the nematode Caenorhabditis elegans. From 56 worm lines that carry mutations induced by the point mutagen ethyl methanesulfonate (EMS), we selected 19 lines that are relatively high in fitness and estimated the viabilities, productivities, and relative fitnesses of heterozygotes and homozygotes compared to the ancestral wild type. There was very little effect of homozygous or heterozygous mutations on egg-to-adult viability. For productivity and relative fitness, we found that the average dominance coefficient, h, was ∼0.1, suggesting that mildly deleterious mutations are on average partially recessive. These estimates were not significantly different from zero (complete recessivity) but were significantly different from 0.5 (additivity). In addition, there was a significant amount of variation in h among lines, and analysis of average dominance coefficients of individual lines suggested that several lines showed overdominance for fitness. Further investigation of two of these lines partially confirmed this finding.
R1 and R2 Retrotransposition and Deletion in the rDNA Loci on the X and Y Chromosomes of Drosophila melanogaster
Authors: Pérez-González César E , Burke William D , Eickbush Thomas H
Published: April 2021

The non-LTR retrotransposons R1 and R2 insert into the 28S rRNA genes of arthropods. Comparisons among Drosophila lineages have shown that these elements are vertically inherited, while studies within species have indicated a rapid turnover of individual copies (elimination of old copies and the insertion of new copies). To better understand the turnover of R1 and R2, 200 retrotranspositions and nearly 100 eliminations have been scored in the Harwich mutation-accumulation lines of Drosophila melanogaster. Because the rDNA arrays in D. melanogaster are present on the X and Y chromosomes and no exchanges were detected in these lines, it was possible to show that R1 retrotranspositions occur predominantly in the male germ line, while R2 retrotranspositions were more evenly divided between the germ lines of both sexes. The rate of elimination of elements from the Y rDNA array was twice that of the X rDNA array with both chromosomal loci containing regions where the rate of elimination was on average eight times higher. Most R1 and R2 eliminations appear to occur by large intrachromosomal events (i.e., loopout events) that involve multiple rDNA units. These findings are interpreted in light of the known abundance of R1 and R2 elements in the X and Y rDNA loci of D. melanogaster.
Mixed-Model Reanalysis of Primate Data Suggests Tissue and Species Biases in Oligonucleotide-Based Gene Expression Profiles
Authors: Hsieh Wen-Ping , Chu Tzu-Ming , Wolfinger Russell D , Gibson Greg
Published: April 2021

An emerging issue in evolutionary genetics is whether it is possible to use gene expression profiling to identify genes that are associated with morphological, physiological, or behavioral divergence between species and whether these genes have undergone positive selection. Some of these questions were addressed in a recent study (Enard  et al. 2002) of the difference in gene expression among human, chimp, and orangutan, which suggested an accelerated rate of divergence in gene expression in the human brain relative to liver. Reanalysis of the Affymetrix data set using analysis of variance methods to quantify the contributions of individuals and species to variation in expression of 12,600 genes indicates that as much as one-quarter of the genome shows divergent expression between primate species at the 5% level. The magnitude of fold change ranges from 1.2-fold up to 8-fold. Similar conclusions apply to reanalysis of Enard  et al.'s (2002) parallel murine data set. However, biases inherent to short oligonucleotide microarray technology may account for some of the tissue and species effects. At high significance levels, more differences were observed in the liver than in the brain in each of the pairwise species comparisons, so it is not clear that expression divergence is accelerated in the human brain. Further, there is an apparent bias toward upregulation of gene expression in the brain in both primates and mice, whereas genes are equally likely to be up- or downregulated in the liver when these species diverge. A small subset of genes that are candidates for adaptive divergence may be identified on the basis of a high ratio of interspecific to intraspecific divergence.
A Conservative Test of Genetic Drift in the Endosymbiotic Bacterium Buchnera: Slightly Deleterious Mutations in the Chaperonin groEL
Authors: Herbeck Joshua T , Funk Daniel J , Degnan Patrick H , Wernegreen Jennifer J
Published: April 2021

The obligate endosymbiotic bacterium Buchnera aphidicola shows elevated rates of sequence evolution compared to free-living relatives, particularly at nonsynonymous sites. Because Buchnera experiences population bottlenecks during transmission to the offspring of its aphid host, it is hypothesized that genetic drift and the accumulation of slightly deleterious mutations can explain this rate increase. Recent studies of intraspecific variation in Buchnera reveal patterns consistent with this hypothesis. In this study, we examine inter- and intraspecific nucleotide variation in groEL, a highly conserved chaperonin gene that is constitutively overexpressed in Buchnera. Maximum-likelihood estimates of nonsynonymous substitution rates across Buchnera species are strikingly low at groEL compared to other loci. Despite this evidence for strong purifying selection on groEL, our intraspecific analysis of this gene documents reduced synonymous polymorphism, elevated nonsynonymous polymorphism, and an excess of rare alleles relative to the neutral expectation, as found in recent studies of other Buchnera loci. Comparisons with Escherichia coli generally show patterns predicted by their differences in Ne. The sum of these observations is not expected under relaxed or balancing selection, selective sweeps, or increased mutation rate. Rather, they further support the hypothesis that drift is an important force driving accelerated protein evolution in this obligate mutualist.
Polymorphism, Recombination and Alternative Unscrambling in the DNA Polymerase α Gene of the Ciliate Stylonychia lemnae (Alveolata; class Spirotrichea)
Authors: Ardell David H , Lozupone Catherine A , Landweber Laura F
Published: April 2021

DNA polymerase α is the most highly scrambled gene known in stichotrichous ciliates. In its hereditary micronuclear form, it is broken into >40 pieces on two loci at least 3 kb apart. Scrambled genes must be reassembled through developmental DNA rearrangements to yield functioning macronuclear genes, but the mechanism and accuracy of this process are unknown. We describe the first analysis of DNA polymorphism in the macronuclear version of any scrambled gene. Six functional haplotypes obtained from five Eurasian strains of Stylonychia lemnae were highly polymorphic compared to Drosophila genes. Another incompletely unscrambled haplotype was interrupted by frameshift and nonsense mutations but contained more silent mutations than expected by allelic inactivation. In our sample, nucleotide diversity and recombination signals were unexpectedly high within a region encompassing the boundary of the two micronuclear loci. From this and other evidence we infer that both members of a long repeat at the ends of the loci provide alternative substrates for unscrambling in this region. Incongruent genealogies and recombination patterns were also consistent with separation of the two loci by a large genetic distance. Our results suggest that ciliate developmental DNA rearrangements may be more probabilistic and error prone than previously appreciated and constitute a potential source of macronuclear variation. From this perspective we introduce the nonsense-suppression hypothesis for the evolution of ciliate altered genetic codes. We also introduce methods and software to calculate the likelihood of hemizygosity in ciliate haplotype samples and to correct for multiple comparisons in sliding-window analyses of Tajima's D.
Caenorhabditis elegans Gαq Regulates Egg-Laying Behavior via a PLCβ-Independent and Serotonin-Dependent Signaling Pathway and Likely Functions Both in the Nervous System and in Muscle
Authors: Bastiani Carol A , Gharib Shahla , Simon Melvin I , Sternberg Paul W
Published: April 2021

egl-30 encodes the single C. elegans ortholog of vertebrate Gαq family members. We analyzed the expression pattern of EGL-30 and found that it is broadly expressed, with highest expression in the nervous system and in pharyngeal muscle. We isolated dominant, gain-of-function alleles of egl-30 as intragenic revertants of an egl-30 reduction-of-function mutation. Using these gain-of-function mutants and existing reduction-of-function mutants, we examined the site and mode of action of EGL-30. On the basis of pharmacological analysis, it has been determined that egl-30 functions both in the nervous system and in the vulval muscles for egg-laying behavior. Genetic epistasis over mutations that eliminate detectable levels of serotonin reveals that egl-30 requires serotonin to regulate egg laying. Furthermore, pharmacological response assays strongly suggest that EGL-30 may directly couple to a serotonin receptor to mediate egg laying. We also examined genetic interactions with mutations in the gene that encodes the single C. elegans homolog of PLCβ and mutations in genes that encode signaling molecules downstream of PLCβ. We conclude that PLCβ functions in parallel with egl-30 with respect to egg laying or is not the major effector of EGL-30. In contrast, PLCβ-mediated signaling is likely downstream of EGL-30 with respect to pharyngeal-pumping behavior. Our data indicate that there are multiple signaling pathways downstream of EGL-30 and that different pathways could predominate with respect to the regulation of different behaviors.
Characterization of a Male-Predominant Antisense Transcript Underexpressed in Hybrids ofDrosophila pseudoobscuraandD. persimilis
Authors: Noor Mohamed A F , Michalak Pawel , Donze David
Published: April 2021

Characterizing genes that are misregulated in hybrids may elucidate the genetic basis of hybrid sterility or other hybrid dysfunctions that contribute to speciation. Previously, a small segment of a male-predominant transcript that is underexpressed in adult male hybrids of Drosophila pseudoobscura and D. persimilis relative to pure species was identified in a differential display screen. Here, we obtained the full sequence of this 1330-bp transcript and determined that it is an antisense message with high sequence similarity to the D. melanogaster TRAP100 gene, part of the Mediator protein complex that regulates transcriptional initiation during development. Both the sense and the antisense messages are transcribed in D. pseudoobscura, but only the sense message (TRAP100) is transcribed in D. melanogaster complex species. Unlike the antisense message, the sense message is transcribed similarly in D. pseudoobscura males and females and in hybrids of D. pseudoobscura and D. persimilis. The high sequence similarity between distantly related species suggests that the sense message is functionally constrained within the genus. We speculate that the antisense transcript may have evolved a role in male-specific post-transcriptional regulation of TRAP100 in the D. pseudoobscura lineage and that its underexpression in sterile hybrid males may cause an overproduction of TRAP100 protein, possibly yielding deleterious effects.
Alternative Genetic Foundations for a Key Social Polymorphism in Fire Ants
Authors: Ross Kenneth G , Krieger Michael J B , Shoemaker D DeWayne
Published: April 2021

Little is known about the genetic foundations of colony social organization. One rare example in which a single major gene is implicated in the expression of alternative social organizations involves the presumed odorant-binding protein gene Gp-9 in fire ants. Specific amino acid substitutions in this gene invariably are associated with the expression of monogyny (single queen per colony) or polygyny (multiple queens per colony) in fire ant species of the Solenopsis richteri clade. These substitutions are hypothesized to alter the abilities of workers to recognize queens and thereby regulate their numbers in a colony. We examined whether these same substitutions underlie the monogyny/polygyny social polymorphism in the distantly related fire ant S. geminata. We found that Gp-9 coding region sequences are identical in the polygyne and monogyne forms of this species, disproving our hypothesis that one or a few specific amino acid replacements in the protein are necessary to induce transitions in social organization in fire ants. On the other hand, polygyne S. geminata differs genetically from the monogyne form in ways not mirrored in the two forms of S. invicta, a well-studied member of the S. richteri clade, supporting the conclusion that polygyny did not evolve via analogous routes in the two lineages. Specifically, polygyne S. geminata has lower genetic diversity and different gene frequencies than the monogyne form, suggesting that the polygyne form originated via a founder event from a local monogyne population. These comparative data suggest an alternative route to polygyny in S. geminata in which loss of allelic variation at genes encoding recognition cues has led to a breakdown in discrimination abilities and the consequent acceptance of multiple queens in colonies.
Nucleotide Variation of the Est-6 Gene Region in Natural Populations of Drosophila melanogaster
Authors: Balakirev Evgeniy S , Ayala Francisco J
Published: April 2021

We have investigated nucleotide polymorphism in the Est-6 gene region in four samples of Drosophila melanogaster derived from natural populations of East Africa (Zimbabwe), Europe (Spain), North America (California), and South America (Venezuela). There are two divergent sequence types in the North and South American samples, which are not perfectly (North America) or not at all (South America) associated with the Est-6 allozyme variation. Less pronounced or no sequence dimorphism occurs in the European and African samples, respectively. The level of nucleotide diversity is highest in the African sample, lower (and similar to each other) in the samples from Europe and North America, and lowest in the sample from South America. The extent of linkage disequilibrium is low in Africa (1.23% significant associations), but much higher in non-African populations (22.59, 21.45, and 37.68% in Europe, North America, and South America, respectively). Tests of neutrality with recombination are significant in non-African samples but not significant in the African sample. We propose that demographic history (bottleneck and admixture of genetically different populations) is the major factor shaping the nucleotide patterns in the Est-6 gene region. However, positive selection modifies the pattern: balanced selection creates elevated levels of nucleotide variation around functionally important (target) polymorphic sites (RsaI–/RsaI+ in the promoter region and F/S in the coding region) in both African and non-African samples; and directional selection, acting during the geographic expansion phase of D. melanogaster, creates an excess of very similar sequences (RsaI– and S allelic lineages, in the promoter and coding regions, respectively) in the non-African samples.
Hedgehog Signaling in the Drosophila Eye and Head: An Analysis of the Effects of Different patched Trans-heterozygotes
Authors: Thomas Chloe , Ingham Philip W
Published: April 2021

Characterization of different alleles of the Hedgehog receptor patched (ptc) indicates that they can be grouped into several classes. Most mutations result in complete loss of Ptc function. However, missense mutations located within the putative sterol-sensing domain (SSD) or C terminus of ptc encode antimorphic proteins that are unable to repress Smo activity and inhibit wild-type Ptc from doing so, but retain the ability to bind and sequester Hh. Analysis of the eye and head phenotypes of Drosophila melanogaster in various ptc/ptctuf1 heteroallelic combinations shows that these two classes of ptc allele can be easily distinguished by their eye phenotype, but not by their head phenotype. Adult eye size is inversely correlated with head vertex size, suggesting an alteration of cell fate within the eye-antennal disc. A balance between excess cell division and cell death in the mutant eye discs may also contribute to final eye size. In addition, contrary to results reported recently, the role of Hh signaling in the Drosophila head vertex appears to be primarily in patterning rather than in proliferation, with Ptc and Smo having opposing effects on formation of medial structures.
TheDrosophila melanogasterDNALigase IVGene Plays a Crucial Role in the Repair of Radiation-Induced DNA Double-Strand Breaks and Acts Synergistically WithRad54
Authors: Gorski Marcin M , Eeken Jan C J , de Jong Anja W M , Klink Ilse , Loos Marjan , Romeijn Ron J , van Veen Bert L , Mullenders Leon H , Ferro Wouter , Pastink Albert
Published: April 2021

DNA Ligase IV has a crucial role in double-strand break (DSB) repair through nonhomologous end joining (NHEJ). Most notably, its inactivation leads to embryonic lethality in mammals. To elucidate the role of DNA Ligase IV (Lig4) in DSB repair in a multicellular lower eukaryote, we generated viable Lig4-deficient Drosophila strains by P-element-mediated mutagenesis. Embryos and larvae of mutant lines are hypersensitive to ionizing radiation but hardly so to methyl methanesulfonate (MMS) or the crosslinking agent cis-diamminedichloroplatinum (cisDDP). To determine the relative contribution of NHEJ and homologous recombination (HR) in Drosophila, Lig4; Rad54 double-mutant flies were generated. Survival studies demonstrated that both HR and NHEJ have a major role in DSB repair. The synergistic increase in sensitivity seen in the double mutant, in comparison with both single mutants, indicates that both pathways partially overlap. However, during the very first hours after fertilization NHEJ has a minor role in DSB repair after exposure to ionizing radiation. Throughout the first stages of embryogenesis of the fly, HR is the predominant pathway in DSB repair. At late stages of development NHEJ also becomes less important. The residual survival of double mutants after irradiation strongly suggests the existence of a third pathway for the repair of DSBs in Drosophila.