Abstract:
:This study was designed to characterize further the nontranscribed intergenic spacers (NTSs) of the 5S rRNA genes of fish and evaluate this marker as a tool for comparative studies. Two members of the closely related North American Great Lakes cisco species complex (Coregonus artedi and C. zenithicus) were chosen for comparison. Fluorescence in situ hybridization found the ciscoes to have a single multicopy 5S locus located in a C band-positive region of the largest submetacentric chromosome. The entire NTS was amplified from the two species by polymerase chain reaction with oligonucleotide primers anchored in the conserved 5S coding region. Complete sequences were determined for 25 clones from four individuals representing two discrete NTS length variants. Sequence analysis found the length variants to result from presence of a 130-bp direct repeat. No two sequences from a single fish were identical. Examination of sequence from the coding region revealed two types of 5S genes in addition to pseudogenes. This suggests the presence of both somatic and germline (oocyte) forms of the 5S gene in the genome of Coregonus. The amount of variation present among NTS sequences indicates that accumulation of variation (mutation) is greater in this multicopy gene than is gene conversion (homogenization). The high level of sequence variation makes the 5S NTS an inappropriate DNA sequence for comparisons of closely related taxa.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Sajdak SL,Reed KM,Phillips RBdoi
10.1007/pl00006348subject
Has Abstractpub_date
1998-06-01 00:00:00pages
680-8issue
6eissn
0022-2844issn
1432-1432journal_volume
46pub_type
杂志文章abstract::The homeobox gene Hoxa-13 codes for a transcription factor involved in multiple functions, including body axis and hand/foot development in tetrapods. In this study we investigate whether the loss of one function (e.g., limb loss in snakes) left a molecular footprint in exon 1 of Hoxa-13 that could be associated with ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-008-9156-7
更新日期:2008-12-01 00:00:00
abstract::A major goal of evolutionary biology is to understand how beneficial mutations translate into increased fitness. Here, we study beneficial mutations that arise in experimental populations of yeast evolved in glucose-rich media. We find that fitness increases are caused by enhanced maximum growth rate (R) that come at ...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-018-9829-9
更新日期:2018-02-01 00:00:00
abstract::The alpha-esterase cluster of D. melanogaster contains 11 esterase genes dispersed over 60 kb. Embedded in the cluster are two unrelated open reading frames that have sequence similarity with genes encoding ubiquitin-conjugating enzyme and tropomyosin. The esterase amino acid sequences show 37-66% identity with one an...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02338832
更新日期:1996-09-01 00:00:00
abstract::Single likelihood ancestor counting (SLAC), fixed effects likelihood (FEL), and several random effects likelihood (REL) methods were utilized to identify positively and negatively selected sites in sexually induced gene 1 (Sig1) of four different Thalassiosira species. The SLAC analysis did not find any sites affected...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-006-0016-z
更新日期:2006-08-01 00:00:00
abstract::Many eubacteria contain an ATP-dependent protease complex, which is built by multiple copies of the HslV and HslU proteins and is therefore called HslVU. HslU proteins are AAA + ATPases, while HslV proteins are proteases that show highly significant similarity to beta subunits of proteasomes. Therefore, the HslVU comp...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-005-0282-1
更新日期:2006-10-01 00:00:00
abstract::Previous observations have indicated that Drosophila DNA contains a component that evolves so rapidly that it fails to hybridize between the DNAs of sibling species. To establish the reality of this component and study its properties, the fraction (about 20%) of Drosophila simulans (Dsim) DNA that fails to hybridize t...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02099998
更新日期:1990-03-01 00:00:00
abstract::Statistical and biochemical studies of the genetic code have found evidence of nonrandom patterns in the distribution of codon assignments. It has, for example, been shown that the code minimizes the effects of point mutation or mistranslation: erroneous codons are either synonymous or code for an amino acid with chem...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006381
更新日期:1998-09-01 00:00:00
abstract::Group selection is a matter of acute controversy among evolutionary biologists. The most well-publicized debate in this regard is that between Edward O. Wilson and Richard Dawkins. As is widely known, Edward O. Wilson is very excited about the idea of social selection and eusociality; by contrast Richard Dawkins favor...
journal_title:Journal of molecular evolution
pub_type: 社论
doi:10.1007/s00239-018-9841-0
更新日期:2018-04-01 00:00:00
abstract::Genes encoding the olfactory receptors of the "OR37" subfamily of the mouse are characterized by special features including a clustered expression pattern, assembly in two distinct gene clusters, and highly conserved putative promoter motifs. Mining the rat and dog databases revealed that these two species possess hig...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-005-0093-4
更新日期:2006-04-01 00:00:00
abstract::The 5S ribosomal RNA sequences have been determined for the rhodoplast of the red alga Porphyra umbilicalis and the chloroplast of the conifer Juniperus media. The 5S RNA sequence of the Vicia faba chloroplast is corrected with respect to a previous report. A survey of the known sequences and secondary structures of 5...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02138372
更新日期:1988-01-01 00:00:00
abstract::In the plant chloroplast genome the codon usage of the highly expressed psbA gene is unique and is adapted to the tRNA population, probably due to selection for translation efficiency. In this study the role of selection on codon usage in each of the fully sequenced chloroplast genomes, in addition to Chlamydomonas re...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006325
更新日期:1998-04-01 00:00:00
abstract::Available molecular and biochemical data offer conflicting evidence for the origin of the cyanelle of Cyanophora paradoxa. We show that the similarity of cyanelle and green chloroplast sequences is probably a result of these two lineages independently developing the same pattern of directional nucleotide change (subst...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00182392
更新日期:1992-02-01 00:00:00
abstract::We investigated the molecular evolution of duplicated color vision genes (LWS-1 and SWS2) within cyprinid fish, focusing on the most cavefish-rich genus--Sinocyclocheilus. Maximum likelihood-based codon substitution approaches were used to analyze the evolution of vision genes. We found that the duplicated color visio...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-009-9283-9
更新日期:2009-10-01 00:00:00
abstract::In this article, we investigated the structural and dynamical evolutionary behaviour of a set of ten thioredoxin proteins as formed by three extant forms and seven resurrected ones in laboratory. Starting from the crystallographic structures, we performed all-atom molecular dynamics simulations and compare the traject...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-019-09894-4
更新日期:2019-07-01 00:00:00
abstract::Two types of gene encoding small subunits (SSU) of ADP-glucose pyrophosphorylase, a starch-biosynthetic enzyme, have been found in cereals and other grasses. One of these genes encodes two SSU proteins. These are targeted to different subcellular compartments and expressed in different organs of the plant: the endospe...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-007-9013-0
更新日期:2007-09-01 00:00:00
abstract::Calmodulin is a calcium-binding EF-hand protein that is an activator of many enzymes as well as ion pumps and channels. Due to its multiple targets and its central role in the cell, understanding the evolutionary history of calmodulin genes should provide insights into the origin of genetic complexity in eukaryotes. W...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s002390010074
更新日期:2000-08-01 00:00:00
abstract::Mutational bias toward expansion or contraction of simple sequence repeats (SSRs) is referred to as directionality of SSR evolution. In this communication, we report the mutational bias exhibited by mononucleotide SSRs occurring in the non-coding regions of several prokaryotic genomes. Our investigations revealed that...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-012-9491-6
更新日期:2012-04-01 00:00:00
abstract::We examined the cis- vs. trans-splicing status of the mitochondrial group II intron nad1i728 in 439 species (427 genera) of land plants, using both Southern hybridization results (for 416 species) and intron sequence data from the literature. A total of 164 species (157 genera), all angiosperms, was found to have a tr...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-004-2606-y
更新日期:2004-07-01 00:00:00
abstract::Tests for positive selection have mostly been developed to look for diversifying selection where change away from the current amino acid is often favorable. However, in many cases we are interested in directional selection where there is a shift toward specific amino acids, resulting in increased fitness in the specie...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-016-9765-5
更新日期:2017-01-01 00:00:00
abstract::Eight new examples of retrotransposons of the Gypsy/Ty3 class have been identified in marine species. A 525-nt pol gene-coding region was amplified using degenerate primers from highly conserved regions and has extended the range of recognition of Gypsy/Ty3 far beyond those previously known. The following matrix shows...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00166592
更新日期:1995-01-01 00:00:00
abstract::Copia is a retrotransposon that appears to be distributed widely among the Drosophilidae subfamily. Evolutionary analyses of regulatory regions have indicated that the Copia retrotransposon evolved through both positive and purifying selection, and that horizontal transfer (HT) could also explain its patchy distributi...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-011-9435-6
更新日期:2011-03-01 00:00:00
abstract::There have been two distinct phases of evolution of the genetic code: an ancient phase--prior to the divergence of the three domains of life, during which the standard genetic code was established--and a modern phase, in which many alternative codes have arisen in specific groups of genomes that differ only slightly f...
journal_title:Journal of molecular evolution
pub_type: 杂志文章,评审
doi:10.1007/s00239-015-9686-8
更新日期:2015-06-01 00:00:00
abstract::We have studied the metal-ion catalysis of a number of reactions of the isomers of ImpGpG on a poly(C) template. In the absence of a catalytic metal ion, oligomers at least up to (pG)20 are obtained from the ImpGpG isomers in a 1-methylimidazole buffer. The Pb2+ ion improves the yield of longer oligomers and changes s...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF01795752
更新日期:1981-01-01 00:00:00
abstract::Heterokonts are evolutionarily important as the most nutritionally diverse eukaryote supergroup and the most species-rich branch of the eukaryotic kingdom Chromista. Ancestrally photosynthetic/phagotrophic algae (mixotrophs), they include several ecologically important purely heterotrophic lineages, all grossly unders...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-004-0353-8
更新日期:2006-04-01 00:00:00
abstract::Seven new Italian and two new British HTLV-II isolates were obtained from injecting drug users and the entire long terminal repeat (LTR) region was sequenced. Restriction analysis showed that all the Italian isolates are of the IIb subtype, whereas the British isolates are of the IIa subtype. To understand whether the...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/pl00006340
更新日期:1998-05-01 00:00:00
abstract::In order to assess the roles of gene conversion followed by natural selection and balancing selection for point mutations in polymorphisms at major histocompatibility complex (MHC) loci, DNA sequences of several mammalian taxa were analyzed. Synonymous and nonsynonymous diversities were estimated separately for the an...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00170662
更新日期:1995-08-01 00:00:00
abstract::Segmental pattern in Drosophila melanogaster is set up via a set of cell-cell interactions mediated by the products of the segment polarity genes. Among these is the armadillo gene, whose product seems to be required for the reception of an intercellular signal encoded by the wingless gene. As part of our effort to re...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00160477
更新日期:1993-03-01 00:00:00
abstract::The usage of synonymous codons and the frequencies of amino acids were investigated in the complete genome of the bacterium Thermotoga maritima using a multivariate statistical approach. The GC3 content of each gene was the most prominent source of variation of codon usage. Surprisingly the usage of UGU and UGC (synon...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/s00239-001-0040-y
更新日期:2002-05-01 00:00:00
abstract::Algae are a heterogeneous group of photosynthetic eukaryotes traditionally separated into three major subdivisions: rhodophytes, chlorophytes, and chromophytes. The evolutionary origin of rhodophytes or red algae and their links to other photosynthetic and nonphotosynthetic eukaryotes have been a matter of much contro...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF00163149
更新日期:1994-04-01 00:00:00
abstract::We have determined the nucleotide sequence of the 26S large subunit (LSU) rRNA genes for two Tetrahymena species, T. thermophila and T. pyriformis. The inferred rRNA sequences are presented in their most probable secondary structures based on compensatory mutations, energy, and conservation criteria. The majority of t...
journal_title:Journal of molecular evolution
pub_type: 杂志文章
doi:10.1007/BF02101107
更新日期:1990-06-01 00:00:00