bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantitative Genetic Models for Describing Simultaneous and Recursive Relationships Between PhenotypesThis article is dedicated to Arthur B. Chapman, teacher and mentor of numerous animal breeding students and disciple and friend of Sewall Wright.
Authors: Gianola Daniel , Sorensen Daniel 
Published: August 2004

AbstractMultivariate models are of great importance in theoretical and applied quantitative genetics. We extend quantitative genetic theory to accommodate situations in which there is linear feedback or recursiveness between the phenotypes involved in a multivariate system, assuming an infinitesimal, additive, model of inheritance. It is shown that structural parameters defining a simultaneous or recursive system have a bearing on the interpretation of quantitative genetic parameter estimates (e.g., heritability, offspring-parent regression, genetic correlation) when such features are ignored. Matrix representations are given for treating a plethora of feedback-recursive situations. The likelihood function is derived, assuming multivariate normality, and results from econometric theory for parameter identification are adapted to a quantitative genetic setting. A Bayesian treatment with a Markov chain Monte Carlo implementation is suggested for inference and developed. When the system is fully recursive, all conditional posterior distributions are in closed form, so Gibbs sampling is straightforward. If there is feedback, a Metropolis step may be embedded for sampling the structural parameters, since their conditional distributions are unknown. Extensions of the model to discrete random variables and to nonlinear relationships between phenotypes are discussed.
Estimating Recombination Rates Using Three-Site Likelihoods
Authors: Wall Jeffrey D 
Published: August 2004

Abstract
We introduce a new method for jointly estimating crossing-over and gene conversion rates using sequence polymorphism data. The method calculates probabilities for subsets of the data consisting of three segregating sites and then forms a composite likelihood by multiplying together the probabilities of many subsets. Simulations show that this new method performs better than previously proposed methods for estimating gene conversion rates, but that all methods require large amounts of data to provide reliable estimates. While existing methods can easily estimate an “average” gene conversion rate over many loci, they cannot reliably estimate gene conversion rates for a single region of the genome.
Redistribution of Gene Frequency and Changes of Genetic Variation Following a Bottleneck in Population Size
Authors: Zhang Xu-Sheng , Wang Jinliang , Hill William G 
Published: August 2004

Abstract
Although the distribution of frequencies of genes influencing quantitative traits is important to our understanding of their genetic basis and their evolution, direct information from laboratory experiments is very limited. In theory, different models of selection and mutation generate different predictions of frequency distributions. When a large population at mutation-selection balance passes through a rapid bottleneck in size, the frequency distribution of genes is dramatically altered, causing changes in observable quantities such as the mean and variance of quantitative traits. We investigate the gene frequency distribution of a population at mutation-selection balance under a joint-effect model of real stabilizing and pleiotropic selection and its redistribution and thus changes of the genetic properties of metric and fitness traits after the population passes a rapid bottleneck and expands in size. If all genes that affect the trait are neutral with respect to fitness, the additive genetic variance (VA) is always reduced by a bottleneck in population size, regardless of their degree of dominance. For genes that have been under selection, VA increases following a bottleneck if they are (partially) recessive, while the dominance variance increases substantially for any degree of dominance. With typical estimates of mutation parameters, the joint-effect model can explain data from laboratory experiments on the effect of bottlenecking on fitness and morphological traits, providing further support for it as a plausible mechanism for maintenance of quantitative genetic variation.
Caenorhabditis elegans lin-35/Rb, efl-1/E2F and Other Synthetic Multivulva Genes Negatively Regulate the Anaphase-Promoting Complex Gene mat-3/APC8
Authors: Garbe David , Doto Jeffrey B , Sundaram Meera V 
Published: August 2004

Abstract
Retinoblastoma (Rb)/E2F complexes repress expression of many genes important for G1-to-S transition, but also appear to regulate gene expression at other stages of the cell cycle. In C. elegans, lin-35/Rb and other synthetic Multivulva (SynMuv) group B genes function redundantly with other sets of genes to regulate G1/S progression, vulval and pharyngeal differentiation, and other unknown processes required for viabilty. Here we show that lin-35/Rb, efl-1/E2F, and other SynMuv B genes negatively regulate a component of the anaphase-promoting complex or cyclosome (APC/C). The APC/C is a multisubunit complex that promotes metaphase-to-anaphase progression and G1 arrest by targeting different substrates for ubiquitination and proteasome-mediated destruction. The C. elegans APC/C gene mat-3/APC8 has been defined by temperature-sensitive embryonic lethal alleles that strongly affect germline meiosis and mitosis but only weakly affect somatic development. We describe severe nonconditional mat-3 alleles and a hypomorphic viable allele (ku233), all of which affect postembryonic cell divisions including those of the vulval lineage. The ku233 lesion is located outside of the mat-3 coding region and reduces mat-3 mRNA expression. Loss-of-function alleles of lin-35/Rb and other SynMuv B genes suppress mat-3(ku233) defects by restoring mat-3 mRNA to wild-type levels. Therefore, Rb/E2F complexes appear to repress mat-3 expression.
The Genetic Covariance Among Clinal Environments After Adaptation to an Environmental Gradient in Drosophila serrata
Authors: Sgrò Carla M , Blows Mark W 
Published: August 2004

Abstract
We examined the genetic basis of clinal adaptation by determining the evolutionary response of life-history traits to laboratory natural selection along a gradient of thermal stress in Drosophila serrata. A gradient of heat stress was created by exposing larvae to a heat stress of 36° for 4 hr for 0, 1, 2, 3, 4, or 5 days of larval development, with the remainder of development taking place at 25°. Replicated lines were exposed to each level of this stress every second generation for 30 generations. At the end of selection, we conducted a complete reciprocal transfer experiment where all populations were raised in all environments, to estimate the realized additive genetic covariance matrix among clinal environments in three life-history traits. Visualization of the genetic covariance functions of the life-history traits revealed that the genetic correlation between environments generally declined as environments became more different and even became negative between the most different environments in some cases. One exception to this general pattern was a life-history trait representing the classic trade-off between development time and body size, which responded to selection in a similar genetic fashion across all environments. Adaptation to clinal environments may involve a number of distinct genetic effects along the length of the cline, the complexity of which may not be fully revealed by focusing primarily on populations at the ends of the cline.
Comparative Evaluation of a New Effective Population Size Estimator Based on Approximate Bayesian Computation
Authors: Tallmon David A , Luikart Gordon , Beaumont Mark A 
Published: August 2004

Abstract
We describe and evaluate a new estimator of the effective population size (Ne), a critical parameter in evolutionary and conservation biology. This new “SummStat” Ne estimator is based upon the use of summary statistics in an approximate Bayesian computation framework to infer Ne. Simulations of a Wright-Fisher population with known Ne show that the SummStat estimator is useful across a realistic range of individuals and loci sampled, generations between samples, and Ne values. We also address the paucity of information about the relative performance of Ne estimators by comparing the SummStat estimator to two recently developed likelihood-based estimators and a traditional moment-based estimator. The SummStat estimator is the least biased of the four estimators compared. In 32 of 36 parameter combinations investigated using initial allele frequencies drawn from a Dirichlet distribution, it has the lowest bias. The relative mean square error (RMSE) of the SummStat estimator was generally intermediate to the others. All of the estimators had RMSE &gt; 1 when small samples (n = 20, five loci) were collected a generation apart. In contrast, when samples were separated by three or more generations and Ne ≤ 50, the SummStat and likelihood-based estimators all had greatly reduced RMSE. Under the conditions simulated, SummStat confidence intervals were more conservative than the likelihood-based estimators and more likely to include true Ne. The greatest strength of the SummStat estimator is its flexible structure. This flexibility allows it to incorporate any potentially informative summary statistic from population genetic data.
Evidence for Nucleolus Organizer Regions as the Units of Regulation in Nucleolar Dominance in Arabidopsis thaliana Interecotype Hybrids
Authors: Lewis Michelle S , Cheverud James M , Pikaard Craig S 
Published: August 2004

Abstract
Nucleolar dominance describes the silencing of one parent's ribosomal RNA (rRNA) genes in a genetic hybrid. In Arabidopsis thaliana, rRNA genes are clustered in two nucleolus organizer regions, NOR2 and NOR4. In F8 recombinant inbreds (RI) of the A. thaliana ecotypes Ler and Cvi, lines that display strong nucleolar dominance inherited a specific combination of NORs, Cvi NOR4 and Ler NOR2. These lines express almost all rRNA from Cvi NOR4. The reciprocal NOR genotype, Ler NOR4/Cvi NOR2, allowed for expression of rRNA genes from both NORs. Collectively, these data reveal that neither Cvi rRNA genes nor NOR4 are always dominant. Furthermore, strong nucleolar dominance does not occur in every RI line inheriting Cvi NOR4 and Ler NOR2, indicating stochastic effects or the involvement of other genes segregating in the RI mapping population. A partial explanation is provided by an unlinked locus, identified by QTL analysis, that displays an epistatic interaction with the NORs and affects the relative expression of NOR4 vs. NOR2. Collectively, the data indicate that nucleolar dominance is a complex trait in which NORs, rather than individual rRNA genes, are the likely units of regulation.
Nucleotide Variation in the Egfr Locus of Drosophila melanogaster
Authors: Palsson Arnar , Rouse Ann , Riley-Berger Rebecca , Dworkin Ian , Gibson Greg 
Published: August 2004

Abstract
The Epidermal growth factor receptor is an essential gene with diverse pleiotropic roles in development throughout the animal kingdom. Analysis of sequence diversity in 10.9 kb covering the complete coding region and 6.4 kb of potential regulatory regions in a sample of 250 alleles from three populations of Drosophila melanogaster suggests that the intensity of different population genetic forces varies along the locus. A total of 238 independent common SNPs and 20 indel polymorphisms were detected, with just six common replacements affecting &gt;1475 amino acids, four of which are in the short alternate first exon. Sequence diversity is lowest in a 2-kb portion of intron 2, which is also highly conserved in comparison with D. simulans and D. pseudoobscura. Linkage disequilibrium decays to background levels within 500 bp of most sites, so haplotypes are generally restricted to up to 5 polymorphisms. The two North American samples from North Carolina and California have diverged in allele frequency at a handful of individual SNPs, but a Kenyan sample is both more divergent and more polymorphic. The effect of sample size on inference of the roles of population structure, uneven recombination, and weak selection in patterning nucleotide variation in the locus is discussed.
A Role for DNA Polymerase δ in Gene Conversion and Crossing Over During Meiosis in Saccharomyces cerevisiae
Authors: Maloisel Laurent , Bhargava Jaya , Roeder G Shirleen 
Published: August 2004

Abstract
A screen for mutants of budding yeast defective in meiotic gene conversion identified a novel allele of the POL3 gene. POL3 encodes the catalytic subunit of DNA polymerase δ, an essential DNA polymerase involved in genomic DNA replication. The new allele, pol3-ct, specifies a protein missing the last four amino acids. pol3-ct shows little or no defect in DNA replication, but displays a reduction in the length of meiotic gene conversion tracts and a decrease in crossing over. We propose a model in which DNA synthesis determines the length of strand exchange intermediates and influences their resolution toward crossing over.
Selective and Mutational Patterns Associated With Gene Expression in Humans
Authors: Comeron Josep M 
Published: August 2004

Abstract
We report the results of a comprehensive study of the influence of gene expression on synonymous codons, amino acid composition, and intron presence and size in human protein-coding genes. First, in addition to a strong effect of isochores, we have detected the influence of transcription-associated mutational biases (TAMB) on gene composition. Genes expressed in different tissues show diverse degrees of TAMB, with genes expressed in testis showing the greatest influence. Second, the study of tissues with no evidence of TAMB reveals a consistent set of optimal synonymous codons favored in highly expressed genes. This result exposes the consequences of natural selection on synonymous composition to increase efficiency of translation in the human lineage. Third, overall amino acid composition of proteins closely resembles tRNA abundance but there is no difference in amino acid composition in differentially expressed genes. Fourth, there is a negative relationship between expression and CDS length. Significantly, this is observed only among genes with introns, suggesting that the cause for this relationship in humans cannot be associated only with costs of amino acid biosynthesis. Fifth, we show that broadly and highly expressed genes have more, although shorter, introns. The selective advantage for having more introns in highly expressed genes is likely counterbalanced by containment of transcriptional costs and a minimum exon size for proper splicing.
The BDGP Gene Disruption Project
Authors: Bellen Hugo J , Levis Robert W , Liao Guochun , He Yuchun , Carlson Joseph W , Tsang Garson , Evans-Holm Martha , Hiesinger P Robin , Schulze Karen L , Rubin Gerald M , Hoskins Roger A , Spradling Allan C 
Published: August 2004

Abstract
The Berkeley Drosophila Genome Project (BDGP) strives to disrupt each Drosophila gene by the insertion of a single transposable element. As part of this effort, transposons in &gt;30,000 fly strains were localized and analyzed relative to predicted Drosophila gene structures. Approximately 6300 lines that maximize genomic coverage were selected to be sent to the Bloomington Stock Center for public distribution, bringing the size of the BDGP gene disruption collection to 7140 lines. It now includes individual lines predicted to disrupt 5362 of the 13,666 currently annotated Drosophila genes (39%). Other lines contain an insertion at least 2 kb from others in the collection and likely mutate additional incompletely annotated or uncharacterized genes and chromosomal regulatory elements. The remaining strains contain insertions likely to disrupt alternative gene promoters or to allow gene misexpression. The expanded BDGP gene disruption collection provides a public resource that will facilitate the application of Drosophila genetics to diverse biological problems. Finally, the project reveals new insight into how transposons interact with a eukaryotic genome and helps define optimal strategies for using insertional mutagenesis as a genomic tool.
Modification of an Existing Chromosomal Inversion to Engineer a Balancer for Mouse Chromosome 15
Authors: Chick Wallace S H , Mentzer Sarah E , Carpenter Donald A , Rinchik Eugene M , You Yun 
Published: August 2004

Abstract
Chromosomal inversions are valuable genetic tools for mutagenesis screens, where appropriately marked inversions can be used as balancer chromosomes to recover and maintain mutations in the corresponding chromosomal region. For any inversion to be effective as a balancer, it should exhibit both dominant and recessive visible traits; ideally the recessive trait should be a fully penetrant lethality in which inversion homozygotes die before birth. Unfortunately, most inversions recovered by classical radiation or chemical mutagenesis techniques do not have an overt phenotype in either the heterozygous or the homozygous state. However, they can be modified by relatively simple procedures to make them suitable as an appropriately marked balancer. We have used homologous recombination to modify, in embryonic stem cells, the recessive-lethal In(15)21Rk inversion to endow it with a dominant-visible phenotype. Several ES cell lines were derived from inversion heterozygotes, and a keratin-14 (K14) promoter-driven agouti minigene was introduced onto the inverted chromosome 15 in the ES cells by gene targeting. Mice derived from the targeted ES cells carry the inverted chromosome 15 and, at the same time, exhibit lighter coat color on their ears and tails, making this modified In(15)21Rk useful as a balancer for proximal mouse chromosome 15.
Clonal Mosaic Analysis of EMPTY PERICARP2 Reveals Nonredundant Functions of the Duplicated HEAT SHOCK FACTOR BINDING PROTEINs During Maize Shoot DevelopmentSequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession no. AY450672.
Authors: Fu Suneng , Scanlon Michael J 
Published: August 2004

Abstract
The paralogous maize proteins EMPTY PERICARP2 (EMP2) and HEAT SHOCK FACTOR BINDING PROTEIN2 (HSBP2) each contain a single recognizable motif: the coiled-coil domain. EMP2 and HSBP2 accumulate differentially during maize development and heat stress. Previous analyses revealed that EMP2 is required for regulation of heat shock protein (hsp) gene expression and also for embryo morphogenesis. Developmentally abnormal emp2 mutant embryos are aborted during early embryogenesis. To analyze EMP2 function during postembryonic stages, plants mosaic for sectors of emp2 mutant tissue were constructed. Clonal sectors of emp2 mutant tissue revealed multiple defects during maize vegetative shoot development, but these sector phenotypes are not correlated with aberrant hsp gene regulation. Furthermore, equivalent phenotypes are observed in emp2 sectored plants grown under heat stress and nonstress conditions. Thus, the function of EMP2 during regulation of the heat stress response can be separated from its role in plant development. The discovery of emp2 mutant phenotypes in postembryonic shoots reveals that the duplicate genes emp2 and hsbp2 encode nonredundant functions throughout maize development. Distinct developmental phenotypes correlated with the developmental timing, position, and tissue layer of emp2 mutant sectors, suggesting that EMP2 has evolved diverse developmental functions in the maize shoot.
The DrosDel Collection
Authors: Ryder Edward , Blows Fiona , Ashburner Michael , Bautista-Llacer Rosa , Coulson Darin , Drummond Jenny , Webster Jane , Gubb David , Gunton Nicola , Johnson Glynnis , O'Kane Cahir J , Huen David , Sharma Punita , Asztalos Zoltan , Baisch Heiko , Schulze Janet , Kube Maria , Kittlaus Kathrin , Reuter Gunter , Maroy Peter , Szidonya Janos , Rasmuson-Lestander Åsa , Ekström Karin , Dickson Barry , Hugentobler Christoph , Stocker Hugo , Hafen Ernst , Lepesant Jean Antoine , Pflugfelder Gert , Heisenberg Martin , Mechler Bernard , Serras Florenci , Corominas Montserrat , Schneuwly Stephan , Preat Thomas , Roote John , Russell Steven 
Published: August 2004

Abstract
We describe a collection of P-element insertions that have considerable utility for generating custom chromosomal aberrations in Drosophila melanogaster. We have mobilized a pair of engineered P elements, p{RS3} and p{RS5}, to collect 3243 lines unambiguously mapped to the Drosophila genome sequence. The collection contains, on average, an element every 35 kb. We demonstrate the utility of the collection for generating custom chromosomal deletions that have their end points mapped, with base-pair resolution, to the genome sequence. The collection was generated in an isogenic strain, thus affording a uniform background for screens where sensitivity to genetic background is high. The entire collection, along with a computational and genetic toolbox for designing and generating custom deletions, is publicly available. Using the collection it is theoretically possible to generate &gt;12,000 deletions between 1 bp and 1 Mb in size by simple eye color selection. In addition, a further 37,000 deletions, selectable by molecular screening, may be generated. We are now using the collection to generate a second-generation deficiency kit that is precisely mapped to the genome sequence.
The Molecular Population Genetics of HIV-1 Group O
Authors: Lemey Philippe , Pybus Oliver G , Rambaut Andrew , Drummond Alexei J , Robertson David L , Roques Pierre , Worobey Michael , Vandamme Anne-Mieke 
Published: August 2004

Abstract
HIV-1 group O originated through cross-species transmission of SIV from chimpanzees to humans and has established a relatively low prevalence in Central Africa. Here, we infer the population genetics and epidemic history of HIV-1 group O from viral gene sequence data and evaluate the effect of variable evolutionary rates and recombination on our estimates. First, model selection tools were used to specify suitable evolutionary and coalescent models for HIV group O. Second, divergence times and population genetic parameters were estimated in a Bayesian framework using Markov chain Monte Carlo sampling, under both strict and relaxed molecular clock methods. Our results date the origin of the group O radiation to around 1920 (1890–1940), a time frame similar to that estimated for HIV-1 group M. However, group O infections, which remain almost wholly restricted to Cameroon, show a slower rate of exponential growth during the twentieth century, explaining their lower current prevalence. To explore the effect of recombination, the Bayesian framework is extended to incorporate multiple unlinked loci. Although recombination can bias estimates of the time to the most recent common ancestor, this effect does not appear to be important for HIV-1 group O. In addition, we show that evolutionary rate estimates for different HIV genes accurately reflect differential selective constraints along the HIV genome.