Abstract:
:We compared the single-nucleotide polymorphisms (SNPs) in humans in 182 housekeeping and 148 tissue-specific genes. SNPs were divided into rare and common polymorphisms based on their frequencies. We found that housekeeping genes tend to be less polymorphic than tissue-specific genes for both rare and common SNPs. Using mouse as a second species for computing sequence divergences, we found no evidence of positive selection: for both housekeeping and tissue-specific genes, the ratio of nonsynonymous to synonymous common SNPs per site showed no significant difference from that of divergence. Similarly, we observed no evidence of positive selection for the 289 and 149 genes that have orthologs available for divergence calculation between humans and chimpanzees and between humans and Old World monkeys, respectively. A comparison with previous SNP studies suggests that approximately 20% of the nonsynonymous SNPs in the human population are nearly neutral and that positive selection in the human genome might not be as frequent as previously thought.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Zhang L,Li WHdoi
10.1093/molbev/msi240subject
Has Abstractpub_date
2005-12-01 00:00:00pages
2504-7issue
12eissn
0737-4038issn
1537-1719pii
msi240journal_volume
22pub_type
杂志文章abstract::The plant MADS-box regulatory gene family includes several loci that control different aspects of inflorescence and floral development. Orthologs to the Arabidopsis thaliana MADS-box floral meristem genes APETALA1 and CAULIFLOWER and the floral organ identity genes APETALA3 and PISTILLATA were isolated from the congen...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026193
更新日期:1999-08-01 00:00:00
abstract::Substitution rates at the three codon positions (r1, r2, and r3) of mammalian mitochondrial genes are in the order of r3 > r1 > r2, and the rate heterogeneity at the three positions, as measured by the shape parameter of the gamma distribution (alpha 1, alpha 2, and alpha 3), is in the order of alpha 3 > alpha 1 > alp...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025930
更新日期:1998-03-01 00:00:00
abstract::Sex-biased gene expression is becoming an increasingly important way to study sexual selection at the molecular genetic level. However, little is known about the timing, persistence, and continuity of gene expression required in the creation of distinct male and female phenotypes, and even less about how sex-specific ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq042
更新日期:2010-07-01 00:00:00
abstract::Over time, natural selection molds every gene into a unique mosaic of sites evolving rapidly or resisting change-an "evolutionary fingerprint" of the gene. Aspects of this evolutionary fingerprint, such as the site-specific ratio of nonsynonymous to synonymous substitution rates (dN/dS), are commonly used to identify ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp260
更新日期:2010-03-01 00:00:00
abstract::Vitamin B(12) (cobalamin) is a dietary requirement for humans because it is an essential cofactor for two enzymes, methylmalonyl-CoA mutase and methionine synthase (METH). Land plants and fungi neither synthesize or require cobalamin because they do not contain methylmalonyl-CoA mutase, and have an alternative B(12)-i...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr124
更新日期:2011-10-01 00:00:00
abstract::At present there is tremendous interest in characterizing the magnitude and distribution of linkage disequilibrium (LD) throughout the human genome, which will provide the necessary foundation for genome-wide LD analyses and facilitate detailed evolutionary studies. To this end, a human high-density single-nucleotide ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg032
更新日期:2003-02-01 00:00:00
abstract::In a striking contrast, matK is one of the most rapidly evolving plastid genes and also one of the few plastid genes to be retained in all nonphotosynthetic plants examined to date. DNA sequences of this region were obtained from photosynthetic and nonphotosynthetic plants of Orobanchaceae and their relatives. The res...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026295
更新日期:2000-12-01 00:00:00
abstract::The plant pathogen Phytophthora infestans emerged in Europe in 1845, triggering the Irish potato famine and massive European potato crop losses that continued until effective fungicides were widely employed in the 20th century. Today the pathogen is ubiquitous, with more aggressive and virulent strains surfacing in re...
journal_title:Molecular biology and evolution
pub_type: 历史文章,信件
doi:10.1093/molbev/msu086
更新日期:2014-06-01 00:00:00
abstract::Multipartite genomes, containing at least two large replicons, are found in diverse bacteria; however, the advantage of this genome structure remains incompletely understood. Here, we perform comparative genomics of hundreds of finished β-proteobacterial genomes to gain insights into the role and emergence of multipar...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msy248
更新日期:2019-03-01 00:00:00
abstract::Rearrangements of mitochondrial DNA gene order have been suggested as a tool for defining the pattern of evolutionary divergence in arthropod taxa. We have employed a combination of highly conserved insect-based polymerase chain reaction (PCR) primers with long-PCR to survey 14 noninsect arthropods for mitochondrial g...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004141
更新日期:2002-06-01 00:00:00
abstract::Long INterspersed Elements-1 (L1s) constitute >17% of the human genome and still actively transpose in it. Characterizing L1 transposition across the genome is critical for understanding genome evolution and somatic mutations. However, to date, L1 insertion and fixation patterns have not been studied comprehensively. ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa194
更新日期:2020-12-16 00:00:00
abstract::Gene unscrambling in spirotrichous ciliates involves massive genome-wide DNA deletion and rearrangement events during development. During each sexual cycle, the somatic nucleus (macronucleus) regenerates from the germ line nucleus (micronucleus). Development of the polyploid somatic genome requires programmed DNA dele...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj089
更新日期:2006-04-01 00:00:00
abstract::Estimation of evolutionary distances from coding sequences must take into account protein-level selection to avoid relative underestimation of longer evolutionary distances. Current modeling of selection via site-to-site rate heterogeneity generally neglects another aspect of selection, namely position-specific amino ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025995
更新日期:1998-07-01 00:00:00
abstract::Seminal fluid proteins (SFPs) mediate an array of postmating reproductive processes that influence fertilization and fertility. As such, it is widely held that SFPs may contribute to postmating, prezygotic reproductive barriers between closely related taxa. We investigated seminal fluid (SF) diversification in a recen...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msz235
更新日期:2020-02-01 00:00:00
abstract::Molluscs in general, and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans. Two factors inhibiting our understanding the evolution of gene rearrangement in bivalves are inadequate taxonomic sampling and failure to examine gene order in a ph...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg218
更新日期:2003-11-01 00:00:00
abstract::Pseudogenes are defined as nonfunctional DNA sequences with homology to functional protein-coding genes, and they typically contain nonfunctional mutations within the presumptive coding region. In theory, pseudogenes can also be caused by mutations in upstream regulatory regions, appearing as open reading frames with ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq298
更新日期:2011-03-01 00:00:00
abstract::Sequencing multiple copies of the ITS1 region revealed the coexistence of two or more haplotypes within the genome of Chorthippus parallelus. Using a PCR-RFLP approach, the ITS1 numbers and frequencies of haplotypes present in each of 40 individuals were investigated, revealing a consistent lack of homogeneity. For ea...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh163
更新日期:2004-08-01 00:00:00
abstract::We describe here a case of homologous introns containing homologous open reading frames (ORFs) that are inserted at the same site in the large subunit (LSU) rRNA gene of different organelles in distantly related organisms. We show that the chloroplast LSU rRNA gene of the green alga Chlamydomonas pallidostigmatica con...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040234
更新日期:1995-07-01 00:00:00
abstract::Indirect tests have detected recombination in mitochondrial DNA (mtDNA) from many animal lineages, including mammals. However, it is possible that features of the molecular evolutionary process without recombination could be incorrectly inferred by indirect tests as being due to recombination. We have identified one s...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr076
更新日期:2011-09-01 00:00:00
abstract::A cDNA that encodes the heart-type lactate dehydrogenase (LDH-B) from the teleost fish Fundulus heteroclitus was cloned and sequenced. The protein encoded by the cDNA was analyzed in relation to 13 LDH proteins from a variety of taxa. One of the deductions from this analysis is that LDH-B proteins have residues in the...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040559
更新日期:1989-07-01 00:00:00
abstract::We determine the phylogenetic backbone of the East Asian mtDNA tree by using published complete mtDNA sequences and assessing both coding and control region variation in 69 Han individuals from southern China. This approach assists in the interpretation of published mtDNA data on East Asians based on either control re...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003996
更新日期:2002-10-01 00:00:00
abstract::In primates, the craniofacial skeleton and the dentition are marked by high levels of interspecific variation. Despite this, there are few comparative species studies conducted at the molecular level to investigate this functional diversity. We have determined nucleotide sequences of MSX1 and PAX9, two developmental g...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msj072
更新日期:2006-03-01 00:00:00
abstract::Genetic incompatibilities are commonly observed between hybridizing species. Although this type of isolating mechanism has received considerable attention, we have few examples describing how genetic incompatibilities evolve. We investigated the evolution of two loci involved in a classic example of a Bateson-Dobzhans...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/mst127
更新日期:2013-10-01 00:00:00
abstract::Plant phenotypic plasticity describes altered phenotypic performance of an individual when grown in different environments. Exploring genetic architecture underlying plant plasticity variation may help mitigate the detrimental effects of a rapidly changing climate on agriculture, but little research has been done in t...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa283
更新日期:2020-11-03 00:00:00
abstract::The transposable element hobo has been introduced into the previously empty Drosophila melanogaster strain Hikone so that its dynamics can be followed and it can be compared with the P element. Five transformed lines were followed over 58 generations. The results were highly dependent on the culture temperature, the s...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040251
更新日期:1995-09-01 00:00:00
abstract::Microarray platforms are used increasingly to make comparative inferences through genome-wide surveys of gene expression. Although recent studies focus on describing the evidence for natural selection using estimates of the within- and between-taxa mutational variances, these methods do not explicitly or flexibly acco...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp149
更新日期:2009-10-01 00:00:00
abstract::The T1 family of retrotransposable elements is interspersed and moderately repeated in five member species of the Anopheles gambiae sibling-species complex and has diverged little since the radiation of the complex. T1 includes two closely related but independent subfamilies, defined by the presence or absence of link...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040599
更新日期:1990-05-01 00:00:00
abstract::Gene orders have been shown to be generally unstable by comprehensive analyses in several complete genomes. In this study, we examined instability of genome structures within operons, where functionally related genes are clustered. We compared gene orders of known operons obtained from Escherichia coli and Bacillus su...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026114
更新日期:1999-03-01 00:00:00
abstract::In all anthropoid species, the coding region of the involucrin gene contains a segment of short tandem repeats that were added sequentially, beginning in a common anthropoid ancestor. The involucrin coding region of each of two platyrrhine species, the white-fronted capuchin (Cebus albifrons) and the cottontop tamarin...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040674
更新日期:1991-09-01 00:00:00
abstract::The internal consistency of the PAM matrix model of protein evolution is here investigated. The 1 PAM matrix has been constructed from amino acid replacements observed in closely related sequences. Such replacements are of two types, those that do not require an intermediate amino acid replacement and those that do. T...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040360
更新日期:1985-09-01 00:00:00