Abstract：
:The simple codominant expression of the alleles at the self-incompatibility locus ( S) of Solanaceae and their extraordinary spectrum of sequence diversity present an ideal case for understanding the molecular forces that shape the sequence polymorphism of genes involved in recognition reactions. Here, with unprecedented conspecific sequences of 33 Physalis longifolia S alleles, including 27 of their single introns, the tempo-spatial nucleotide substitution patterns were first detailed for the S locus and analyzed in genealogical time scales. Three major genealogical clades of the 33 P. longifolia S alleles were used to divide the genealogical time into the within-clade and the between-clade periods. During the within-clade period, the average nonsynonymous substitution rate was 50% higher than the intron substitution rate but the opposite trend emerged for the between-clade period. A new and simple method developed here was utilized to estimate the selection intensity in the coding regions. The magnitudes and the distribution of these estimates, in conjunction with the spatial substitution pattern among closely related S sequences, revealed an initial short-term action of strong positive selection and a continuous but weaker action of negative selection brought by functional/structural constraints on the S alleles. The two modes of selection can significantly modify the branch lengths of an S genealogy and may be ubiquitous to recognition systems.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Lu Ydoi
10.1007/s00239-001-0080-3keywords:
subject
Has Abstractpub_date
2002-06-01 00:00:00pages
784-93issue
6eissn
0022-2844issn
1432-1432journal_volume
54pub_type
杂志文章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：:As illustrated by the mitochondrion and the eukaryotic cell, little in biology makes sense except in light of mutualism. Mutualisms are persistent, intimate, and reciprocal exchanges; an organism proficient in obtaining certain benefits confers those on a partner, which reciprocates by conferring different benefits. M...
journal_title：Journal of molecular evolution
pub_type： 杂志文章,评审
doi：10.1007/s00239-017-9804-x
更新日期：2017-08-01 00:00:00
abstract：:Short interspersed DNA elements (SINEs) amplify by retroposition either by (i) successive waves of amplification from one or a few evolving master genes or by (ii) the generation of new master genes that coexist with their progenitors. Individual, highly conserved, elements of the B1 SINE family were identified from t...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010087
更新日期：2000-09-01 00:00:00
abstract：:Membrane proteins that transport ATP and ADP have been identified in mitochondria, plastids, and obligate intracellular parasites. The mitochondrial ATP/ADP transporters are derived from a broad-specificity transport family of eukaryotic origin, whereas the origin of the plastid/parasite ATP/ADP translocase is more el...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-002-2387-0
更新日期：2003-02-01 00:00:00
abstract：:At least two polymorphic Alu insertions have been previously identified and characterized within the class I region of the major histocompatibility complex (MHC). We have identified another two new polymorphic Alu insertions, AluyHJ and AluyHF, located near HLA-J and HLA-F, respectively, within the a block of the MHC....
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-002-2367-4
更新日期：2002-12-01 00:00:00
abstract：:We have studied the relative contribution of inversions, transpositions, deletions, and nucleotide substitutions to the evolution of Chlamydia trachomatis and Chlamydia pneumoniae. The minimal number of rearrangement events required for converting the gene order structure of one genome into that of the other was estim...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-001-0087-9
更新日期：2002-07-01 00:00:00
abstract：:We have used three reference sequences representative of bacterial drug resistance pumps and sugar transport proteins to collect the 91 most closely related sequences from a composite, nonredundant protein sequence database. Having eliminated certain very close relatives, the remainder were subjected to analysis and a...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02198855
更新日期：1996-02-01 00:00:00
abstract：:The activated dimonophosphate of 3'-deoxyadenosine (cordycepin) undergoes oligomerization to produce a new family of pyrophosphate-linked oligomers in which the average repeating unit involves a nine-atom structural group. The presence of a poly(U) template increases the relative yields of higher oligomers, although t...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02101146
更新日期：1987-01-01 00:00:00
abstract：:The metabolic cycle of Saccharomyces cerevisiae consists of alternating oxidative (respiration) and reductive (glycolysis) energy-yielding reactions. The intracellular concentrations of amino acid precursors generated by these reactions oscillate accordingly, attaining maximal concentration during the middle of their ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-009-9218-5
更新日期：2009-05-01 00:00:00
abstract：:The heterotrophic theory of the origin of life is the only proposal available with experimental support. This comes from the ease of prebiotic synthesis under strongly reducing conditions. The prebiotic synthesis of organic compounds by reduction of CO(2) to monomers used by the first organisms would also be considere...
journal_title：Journal of molecular evolution
pub_type： 杂志文章,评审
doi：
更新日期：1999-10-01 00:00:00
abstract：:A model of nucleotide substitution that allows the transition/transversion rate bias to vary across sites was constructed. We examined the fit of this model using likelihood-ratio tests by analyzing 13 protein coding genes and 1 pseudogene. Likelihood-ratio testing indicated that a model that allows variation in the t...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006448
更新日期：1999-01-01 00:00:00
abstract：:Quantitative immunological comparisons of three avian proteins, transferrin, ovalbumin, and penalbumin, indicate that penguins are phylogenetically most closely related to loons, albatrosses, herons, and grebes. These data support the theory that the ancestors of penguins were flying oceanic birds and that flightlessn...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01731000
更新日期：1976-10-27 00:00:00
abstract：:The present work represents the first attempt to study in greater detail previously proposed compositional correlations in genomes, based on a body of additional data relating to gene localizations as well as to extended flanking sequences extracted from gene banks. We have investigated the correlations that exist bet...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02102651
更新日期：1991-06-01 00:00:00
abstract：:The diversity of functional genes and the related processes are important issues for conservation biology. This is especially relevant for populations that have suffered from demographic reduction as a consequence of the processes of postglacial colonization. In this perspective, the aims of the present study are (1) ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9456-1
更新日期：2011-08-01 00:00:00
abstract：:The human Rh blood group locus consists of two structurally related genes (D and CcEe) in Rh-positive haplotypes but a single gene (CcEe) in Rh-negative haplotypes. The genome of rhesus monkeys (Macaca mulatta), while not expressing any of the human Rh D, C, c, E, or e specificities, carries a Rh-like locus strongly r...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00166163
更新日期：1994-02-01 00:00:00
abstract：:Photosynthetic eukaryotes can, according to features of their chloroplasts, be divided into two major groups: the red and the green lineage of plastid evolution. To extend the knowledge about the evolution of the red lineage we have sequenced and analyzed the chloroplast genome (cp-genome) of Cyanidium caldarium RK1, ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s002390010101
更新日期：2000-10-01 00:00:00
abstract：:In the present study we focus on the nucleotide and the inferred amino acid variation occurring in humans and other primate species for mitochondrial NAD(+)-dependent succinic semialdehyde dehydrogenase, a gene recently supposed to contribute to cognitive performance in humans. We determined 2527 bp of coding, introni...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-005-0154-8
更新日期：2006-07-01 00:00:00
abstract：:Mitochondrial DNA (mtDNA) restriction site maps for nine species of the Drosophila obscura subgroup and for Drosophila melanogaster were established. Taking into account all restriction enzymes (12) and strains (45) analyzed, a total of 105 different sites were detected, which corresponds to a sample of 3.49% of the m...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02109481
更新日期：1990-08-01 00:00:00
abstract：:Oligonucleotide cataloguing has been used to characterize a number of 5S RNA species from various Procaryotes. Such catalogs can be used to establish certain and detailed phylogenetic relationships among organisms. Confining attention at present to four Families of Procaryotes, theEnterobacteriaceae, theBacillaceae, t...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01659163
更新日期：1972-06-01 00:00:00
abstract：:LINE-1 (L1) elements constitute the major family of retrotransposons in mammalian genomes. Here we report the first investigation of L1 evolution in New World monkeys (NWM). Two regions of the second open-reading frame were analyzed by two methods in three NWM species, the squirrel monkey (Saimiri sciureus), the tamar...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-003-2539-x
更新日期：2004-01-01 00:00:00
abstract：:The human S100 gene family encodes the EF-hand superfamily of calcium-binding proteins, with at least 14 family members clustered relatively closely together on chromosome 1q21. We have analyzed the most recently available genomic sequence of the human S100 gene cluster for evidence of tandem gene duplications during ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-002-2410-5
更新日期：2003-04-01 00:00:00
abstract：:Oxygen-free aqueous solutions of NH4CN (0.1 M, pH9) were exposed to gamma rays from a 60Co source, the mixture of nonvolatile products was fractionated, and the fractions were analyzed. The procedures were chosen to make effective investigations of radiolytic products, and to minimize the contributions of chemical cha...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01732951
更新日期：1980-07-01 00:00:00
abstract：:Leucine-rich repeat receptor-like kinases (LRR RLKs) comprise the largest group within the plant receptor-like kinase (RLK) superfamily, and the Arabidopsis genome alone contains over 200 LRR RLK genes. Although there is clear evidence for diverse roles played by individual LRR RLK genes in Arabidopsis growth and deve...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-005-0187-z
更新日期：2006-11-01 00:00:00
abstract：:Hydrophobins are small proteins, characterised by the presence of eight positionally conserved cysteine residues, and are present in all filamentous asco- and basidiomycetes. They are found on the outer surfaces of cell walls of hyphae and conidia, where they mediate interactions between the fungus and the environment...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9438-3
更新日期：2011-04-01 00:00:00
abstract：:MgtC is a virulence factor required for intramacrophage survival and growth in low Mg2+ medium in two pathogens that are not phylogenetically related, Salmonella typhimurium and Mycobacterium tuberculosis. In S. typhimurium, mgtC is carried by the SPI-3 pathogenicity island and hybridization studies have suggested tha...
journal_title：Journal of molecular evolution
pub_type： 信件
doi：10.1007/s00239-003-2496-4
更新日期：2003-10-01 00:00:00
abstract：:We obtained and studied HIV-1 sequences with a known sampling year from three outbreaks of the HIV-1 epidemic: 141 env V3 (270 nt) sampled between 1984 and 1992 and 117 pol prot/RT (804 nt) sequences sampled between 1986 and 1999 from Dutch homosexual men and injecting drug users (IDUs), as well as 77 env V3 sequences...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-001-0070-5
更新日期：2002-05-01 00:00:00
abstract：:DEAD-box proteins are found in all domains of life and participate in almost all cellular processes that involve RNA. The presence of DEAD and Helicase_C conserved domains distinguish these proteins. DEAD-box proteins exhibit RNA-dependent ATPase activity in vitro, and several also show RNA helicase activity. In this ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9441-8
更新日期：2011-04-01 00:00:00
abstract：:All modern mammals contain a distinctive, highly repeated (> or = 50,000 members) family of long interspersed repeated DNA called the L1 (LINE 1) family. While the modern L1 families were derived from a common ancestor that predated the mammalian radiation approximately 80 million years ago, most of the members of the...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02407302
更新日期：1993-01-01 00:00:00
abstract：:We suggest a nucleotide substitution model that takes correlation between base-paired nucleotides into account. The model includes the estimation of the transition-transversion ratio and allows inference of the shape parameter of a discrete gamma distribution to include rate heterogeneity. A Cox-test statistic, applie...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006590
更新日期：1999-11-01 00:00:00
abstract：:In the previous three reports in this series we demonstrated that the EF-hand family of proteins evolved by a complex pattern of gene duplication, transposition, and splicing. The dendrograms based on exon sequences are nearly identical to those based on protein sequences for troponin C, the essential light chain myos...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02406723
更新日期：1993-05-01 00:00:00
