Abstract:
:Positive selection in genes and genomes can point to the evolutionary basis for differences among species and among races within a species. The detection of positive selection can also help identify functionally important protein regions and thus guide protein engineering. Many existing tests for positive selection are excessively conservative, vulnerable to artifacts caused by demographic population history, or computationally very intensive. I here propose a simple and rapid test that is complementary to existing tests and that overcomes some of these problems. It relies on the null hypothesis that neutrally evolving DNA regions should show a Poisson distribution of nucleotide substitutions. The test detects significant deviations from this expectation in the form of variation clusters, highly localized groups of amino acid changes in a coding region. In applying this test to several thousand human-chimpanzee gene orthologs, I show that such variation clusters are not generally caused by relaxed selection. They occur in well-defined domains of a protein's tertiary structure and show a large excess of amino acid replacement over silent substitutions. I also identify multiple new human-chimpanzee orthologs subject to positive selection, among them genes that are involved in reproductive functions, immune defense, and the nervous system.
journal_name
Geneticsjournal_title
Geneticsauthors
Wagner Adoi
10.1534/genetics.107.074732subject
Has Abstractpub_date
2007-08-01 00:00:00pages
2451-63issue
4eissn
0016-6731issn
1943-2631pii
genetics.107.074732journal_volume
176pub_type
杂志文章相关文献
GENETICS文献大全abstract::Cytoplasmic male sterility (CMS), the maternally inherited failure to produce functional pollen, has been used in the breeding of sugar beet (Beta vulgaris ssp. vulgaris). At least three different sources of CMS can be distinguished from one another as well as from normal fertile cytoplasm by polymorphisms in their mi...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.107.076380
更新日期:2007-11-01 00:00:00
abstract::C. elegans spermatogenesis employs lysosome-related fibrous body-membranous organelles (FB-MOs) for transport of many cellular components. Previous work showed that spe-10 mutants contain FB-MOs that prematurely disassemble, resulting in defective transport of FB components into developing spermatids. Consequently, sp...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.105.047340
更新日期:2006-01-01 00:00:00
abstract::A large number of arginine-requiring mutants of Neurospora was isolated, using a strain already partially impaired in an enzyme of the pathway. Among the mutants, all previously described loci, except one, were represented, and several new loci were defined and mapped. Four groups of mutants were of particular interes...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1979-11-01 00:00:00
abstract::Metazoan genomes encode an abundant collection of mRNA-like, long noncoding (lnc)RNAs. Although lncRNAs greatly expand the transcriptional repertoire, we have a limited understanding of how these RNAs contribute to developmental regulation. Here, we investigate the function of the Drosophila lncRNA called yellow-achae...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.111.131706
更新日期:2011-10-01 00:00:00
abstract::Nucleostemin 3 (NS3) is an evolutionarily conserved protein with profound roles in cell growth and viability. Here we analyze cell-autonomous and non-cell-autonomous growth control roles of NS3 in Drosophila and demonstrate its GTPase activity using genetic and biochemical assays. Two null alleles of ns3, and RNAi, de...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.112.149104
更新日期:2013-05-01 00:00:00
abstract::Fifty-eight isochromosomal lines sampled from two natural populations of Drosophila pseudoobscura in California and one from Bogota, Colombia, were examined using four-cutter restriction mapping. A 4.6-kb region of the xanthine dehydrogenase locus was probed and 66 of 135 restriction sites scored were polymorphic. Thi...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1989-10-01 00:00:00
abstract::C4 and CYP21 are two adjacent, but functionally unrelated genes residing in the middle of the mammalian major histocompatibility complex (Mhc). The C4 gene codes for the fourth component of the complement cascade, whereas the CYP21 gene specifies an enzyme (cytochrome P450c21) of the glucocorticoid and mineralocortico...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1993-05-01 00:00:00
abstract::Amoebae of the Colonia (CL) strain, which normally produce plasmodia in clones, are shown to cross with mt3 and mt4 amoebae under appropriate conditions. Strains carrying mt3 and mt4 in a CL genetic background were constructed and used in the genetic analysis of mutants isolated in CL. ...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1974-12-01 00:00:00
abstract::Crossovers (COs) generated through meiotic recombination are important for the correct segregation of homologous chromosomes during meiosis. Several models describing the molecular mechanism of meiotic recombination have been proposed. These models differ in the arrangement of heteroduplex DNA (hDNA) in recombination ...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.107.070367
更新日期:2007-05-01 00:00:00
abstract::Orthologous positions of 55 genes associated with height in four human populations were located on the bovine genome. Single nucleotide polymorphisms close to eight of these genes were significantly associated with stature in cattle (Bos taurus and Bos indicus). This suggests that these genes may contribute to control...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.110.123943
更新日期:2011-03-01 00:00:00
abstract::Mapping quantitative trait loci in plants is usually conducted using a population derived from a cross between two inbred lines. The power of such QTL detection and the parameter estimates depend largely on the choice of the two parental lines. Thus, the QTL detected in such populations represent only a small part of ...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.104.028993
更新日期:2004-11-01 00:00:00
abstract::The transcription factors Adr1 and Cat8 act in concert to regulate the expression of numerous yeast genes after the diauxic shift. Their activities are regulated by Snf1, the yeast homolog of the AMP-activated protein kinase of higher eukaryotes. Cat8 is regulated directly by Snf1, but how Snf1 regulates Adr1 is unkno...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.109.103432
更新日期:2009-07-01 00:00:00
abstract::Centromeres are responsible for the correct segregation of chromosomes during mitosis and meiosis. Holocentric chromosomes, characterized by multiple centromere units along each chromatid, have particular adaptations to ensure regular disjunction during meiosis. Here we show by detecting CENH3, CENP-C, tubulin, and ce...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.116.191213
更新日期:2016-10-01 00:00:00
abstract::Neutrality tests based on the frequency spectrum (e.g., Tajima's D or Fu and Li's F) are commonly used by population geneticists as routine tests to assess the goodness-of-fit of the standard neutral model on their data sets. Here, I show that these neutrality tests are specific instances of a general model that encom...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.109.104042
更新日期:2009-09-01 00:00:00
abstract::In the present study, we investigated intrachromosomal homologous recombination in a murine hybridoma in which the recipient for recombination, the haploid, endogenous chromosomal immunoglobulin mu-gene bearing a mutation in the constant (Cmu) region, was separated from the integrated single copy wild-type donor Cmu r...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1999-06-01 00:00:00
abstract::AFLP markers are becoming one of the most popular tools for genetic analysis in the fields of evolutionary genetics and ecology and conservation of genetic resources. The technique combines a high-information content and fidelity with the possibility of carrying out genomewide scans. However, a potential problem with ...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.107.083246
更新日期:2008-05-01 00:00:00
abstract::Mutant alleles of two genetic regulatory elements, which underlie a three- to sixfold reduction in beta-glucuronidase (GUS) activity levels, distinguish mice of the H haplotype from those of the other two common GUS haplotypes, A and B. Both elements are tightly linked to the GUS structural gene over which they exert ...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1989-01-01 00:00:00
abstract::Though much has been learned about the process of ovarian follicle maturation through studies of oogenesis in both vertebrate and invertebrate systems, less is known about how follicles form initially. In Drosophila, two somatic follicle stem cells (FSCs) in each ovariole give rise to all polar cells, stalk cells, and...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.109.109538
更新日期:2010-02-01 00:00:00
abstract::The relationships between synonymous and nonsynonymous substitution rates and between synonymous rate and codon usage bias are important to our understanding of the roles of mutation and selection in the evolution of Drosophila genes. Previous studies used approximate estimation methods that ignore codon bias. In this...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2001-01-01 00:00:00
abstract::Double-strand DNA breaks can be repaired by any of several alternative mechanisms that differ greatly in the nature of the final repaired products. We used a reporter construct, designated "Repair reporter 3" (Rr3), to measure the relative usage of these pathways in Drosophila germ cells. The method works by creating ...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.105.050138
更新日期:2006-02-01 00:00:00
abstract::Genomic resources for hundreds of species of evolutionary, agricultural, economic, and medical importance are unavailable due to the expense of well-assembled genome sequences and difficulties with multigenerational studies. Teleost fish provide many models for human disease but possess anciently duplicated genomes th...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.111.127324
更新日期:2011-08-01 00:00:00
abstract::We have identified two Saccharomyces cerevisiae genes that, in high copy, confer resistance to Kluyveromyces lactis zymocin, an inhibitor that blocks cells in the G(1) phase of the cell cycle prior to budding and DNA replication. One gene (GRX3) encodes a glutaredoxin and is likely to act at the level of zymocin entry...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2001-12-01 00:00:00
abstract::I report a framework for assessing whether one mitochondrial genome is significantly more rearranged than another. This relative rate of gene rearrangement test (RGR) behaves according to expectation, distinguishing between highly rearranged and mildly rearranged insect mitochondrial genomes. It may be more broadly ap...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.103.024885
更新日期:2004-06-01 00:00:00
abstract::Dispersal is a crucial factor in natural evolution, since it determines the habitat experienced by any population and defines the spatial scale of interactions between individuals. There is compelling evidence for systematic differences in dispersal characteristics within the same population, i.e., genotype-dependent ...
journal_title:Genetics
pub_type: 杂志文章
doi:10.1534/genetics.116.193946
更新日期:2017-01-01 00:00:00
abstract::The genomes of all organisms are subject to continuous bombardment of deleterious genomic mutations (DGM). Our ability to accurately estimate various parameters of DGM has profound significance in population and evolutionary genetics. The Deng-Lynch method can estimate the parameters of DGM in natural selfing and outc...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:2002-11-01 00:00:00
abstract::Specific mutations in the gene encoding the largest subunit of RNA polymerase II (RpII215) cause a partial transformation of a structure of the third thoracic segment, the capitellum, into the analogous structure of the second thoracic segment, the wing. This mutant phenotype is also caused by genetically reducing the...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1992-08-01 00:00:00
abstract::Genic variation in natural populations of Drosophila simulans was surveyed using allozymic and two-dimensional electrophoretic techniques. Consistent with some previous reports, allozymic heterozygosity appeared lower than in the sibling species D. melanogaster (0.07 vs. 0.16). No variation was detected by two-dimensi...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1982-01-01 00:00:00
abstract::The construction in bacteriophage lambda of a set of long DNA palindromes with paired changes in the central sequence is described. Identical palindrome centers were previously used by others to test the S-type model for cruciform extrusion in vitro. Long DNA palindromes prevent the propagation of carrier phage lambda...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1994-06-01 00:00:00
abstract::We examined linkage relationships for RecBC-mediated recombination in lytic cycle crosses of lambda phages bearing two cohesive end sites (cos) oriented in the same direction. The relationships obtained imply that a given recombinant tends to be packaged from the cos site that is the nearer one to the right of the exc...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1986-06-01 00:00:00
abstract::The morphogenetic pathway of bacteriophage phi X 174 was investigated in rep mutant hosts that specifically block stage III single-stranded DNA synthesis. The defects conferred by the mutant rep protein most likely affect the formation or stabilization of the 50S complex, a single-stranded DNA synthesizing intermediat...
journal_title:Genetics
pub_type: 杂志文章
doi:
更新日期:1995-08-01 00:00:00