Abstract：
:The mitochondrial cytochrome b (cyt-b) gene is widely used in systematic studies to resolve divergences at many taxonomic levels. The present study focuses mainly on the utility of cyt-b as a molecular marker for inferring phylogenetic relationship at various levels within the fish family Cichlidae. A total of 78 taxa were used in the present analysis, representing all the major groups in the family Cichlidae (72 taxa) and other families from the suborders Labroidei and Percoidei. Gene trees obtained from cyt-b are compared to a published total evidence tree derived from previous studies. Minimum evolution trees based on cyt-b data resulted in topologies congruent with all previous analyses. Parsimony analyses downweighting transitions relative to transversions (ts1:tv4) or excluding transitions at third codon positions resulted in more robust bootstrap support for recognized clades than unweighted parsimony. Relative rate tests detected significantly long branches for some taxa (LB taxa) which were composed mainly by dwarf Neotropical cichlids. An improvement of the phylogenetic signal, as shown by the four-cluster likelihood mapping analysis, and higher bootstrap values were obtained by excluding LB taxa. Despite some limitations of cyt-b as a phylogenetic marker, this gene either alone or in combination with other data sets yields a tree that is in agreement with the well-established phylogeny of cichlid fish.
journal_name
J Mol Evoljournal_title
Journal of molecular evolutionauthors
Farias IP,Ortí G,Sampaio I,Schneider H,Meyer Adoi
10.1007/s002390010197keywords:
subject
Has Abstractpub_date
2001-08-01 00:00:00pages
89-103issue
2eissn
0022-2844issn
1432-1432journal_volume
53pub_type
杂志文章abstract：:We describe the structure of a gene expressed in the salivary gland cells of the dipteran Chironomus tentans and show that it encodes 1 of the approximately 15 secretory proteins exported by the gland cells. This sp115,140 gene consists of approximately 65 copies of a 42-bp sequence in a central uninterrupted core blo...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02101791
更新日期：1990-07-01 00:00:00
abstract：:A systematic way of inferring evolutionary relatedness of microbial organisms from the oligopeptide content, i.e., frequency of amino acid K-strings in their complete proteomes, is proposed. The new method circumvents the ambiguity of choosing the genes for phylogenetic reconstruction and avoids the necessity of align...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-003-2493-7
更新日期：2004-01-01 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：:We characterized the organization of mitochondrial genes from a diverse range of hymenopterans. Of the 21 taxa characterized, 12 had distinct, derived organizations. Some rearrangements were consistent with the duplication-random loss mechanism, while others were not. Local inversions were relatively common, i.e., rea...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-002-2420-3
更新日期：2003-05-01 00:00:00
abstract：:The evolution of viral genomes has recently attracted considerable attention. We compare the sequences of two large viral genomes, EsV-1 and FirrV-1, belonging to the family of phaeoviruses which infect different species of marine brown algae. Although their genomes differ substantially in size, these viruses share si...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-003-2501-y
更新日期：2003-12-01 00:00:00
abstract：:Complement control proteins (CCPs) contain repeated protein domains, short consensus repeats (SCRs), which must be relevant to diverse functions such as complement activation, coagulation, viral binding, fetal implantation, and self-nonself recognition. Although SCRs share some discontinuous and imperfect motifs, ther...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-2609-8
更新日期：2004-08-01 00:00:00
abstract：:The local stability of unbranched biosynthetic pathways is examined by mathematical analysis and computer simulation using a novel nonlinear formalism that appears to accurately describe biochemical systems. Four factors affecting the stability are examined: strength of feedback inhibition, equalization of the values...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01741242
更新日期：1975-08-05 00:00:00
abstract：:A new type of repeat unit was isolated from Balbiani ring 1 of Chironomus pallidivittatus and designated BR1 beta repeat. It consists of a constant and a subrepeated part, like previously described units belonging to the core blocks of the BR genes. The subrepeated part contains 10-codon subrepeats with an arrangement...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02101191
更新日期：1988-01-01 00:00:00
abstract：:Phylogenetic relationships among eight species of the Drosophila buzzatii species complex (D. mulleri subgroup; D. repleta species group) and D. hamatofila were determined by sequencing the mitochondrial cytochrome oxidase subunit I, II, and III genes. The species examined included members of the martensis cluster (D....
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00173155
更新日期：1995-12-01 00:00:00
abstract：:Minerals may have played a significant role in chemical evolution. In the course of investigating the chemistry of phosphonoacetaldehyde (PAL), an analogue of glycolaldehyde phosphate, we have observed a striking case of catalysis by the layered hydroxide mineral hydrotalcite ([Mg2Al(OH)6][Cl.nH2O]). In neutral or mod...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006406
更新日期：1998-11-01 00:00:00
abstract：:The size and diversity of bacteriophage populations require methodologies to quantitatively study the landscape of phage differences. Statistical approaches are confronted with small genome sizes forbidding significant single-phage analysis, and comparative methods analyzing full phage genomes represent an alternative...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-008-9068-6
更新日期：2008-03-01 00:00:00
abstract：:In this paper we present an iterative character weighting method for the construction of phyletic trees. An initial tree is used to calculate the character weights, which are the number of mutations normalized so that the possible range is corrected for. The weights obtained are used to adjust the tree; this process i...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02101127
更新日期：1990-10-01 00:00:00
abstract：:Computational and experimental attempts tried to characterize a universal core of genes representing the minimal set of functional needs for an organism. Based on the increasing number of available complete genomes, comparative genomics has concluded that the universal core contains < 50 genes. In contrast, experiment...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-005-0250-9
更新日期：2006-12-01 00:00:00
abstract：:Throughout history, remote archipelagos have repeatedly been designated natural laboratories to study evolutionary processes. The extensive, geographically structured, morphological variation within Galápagos' Opuntia cacti has been presumed to be another example of how such processes shape diversity. However, recent ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-011-9434-7
更新日期：2011-03-01 00:00:00
abstract：:Pituitary prolactin, like growth hormone (GH) and several other protein hormones, shows an episodic pattern of molecular evolution in which sustained bursts of rapid change contrast with long periods of slow evolution. A period of rapid change occurred in the evolution of prolactin in primates, leading to marked seque...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-0239-9
更新日期：2005-05-01 00:00:00
abstract：:An emergent problem in the study of pathogen evolution is our ability to determine the extent to which their rapidly evolving genomes recombine. Such information is necessary and essential for locating pathogenicity loci using association studies, and it also directs future screening, therapeutic and vaccination strat...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-003-2543-1
更新日期：2004-03-01 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：:Sequence data from regions of five vertebrate vitellogenin genes were used to examine the frequency, distribution, and mutability of the dinucleotide CpG, the preferred modification site for eukaryotic DNA methyltransferases. The observed level of the CpG dinucleotide in all five genes was markedly lower than that exp...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02101752
更新日期：1987-01-01 00:00:00
abstract：:The gene (fus) coding for elongation factor G (EF-G) of the extremely thermophilic eubacterium Thermotoga maritima was identified and sequenced. The EF-G coding sequence (2046 bp) was found to lie in an operon-like structure between the ribosomal protein S7 gene (rpsG) and the elongation factor Tu (EF-Tu) gene (tuf). ...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02193628
更新日期：1991-08-01 00:00:00
abstract：:We studied the genomic organization of Hox genes in Atlantic salmon (Salmo salar) and made comparisons to that in rainbow trout (Oncorhynchus mykiss), another member of the family Salmonidae. We used these two species to test the hypothesis that the Hox genes would provide evidence for a fourth round of duplication (4...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-004-0338-7
更新日期：2005-11-01 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：:Protamine P1 genes have been sequenced following PCR amplification from 11 mammals representing five major mammalian orders: Rodentia (rat and guinea pig), Carnivora (cat and bear), Proboscidea (elephant), Perissodactyla (horse), and Artiodactyla (camel, deer, elk, moose, and gazelle). The predicted amino acid sequenc...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00160507
更新日期：1995-06-01 00:00:00
abstract：:In the traditional concept for the origin of life as proposed by Oparin and Haldane in the 1920s, prebiotic reactants became slowly concentrated in the primordial oceans and life evolved slowly from a series of highly protracted chemical reactions during the first billion years of Earth's history. However, chemical e...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF02102187
更新日期：1991-01-01 00:00:00
abstract：:Abortive cycling features transcription initiation by RNA polymerase in both prokaryote and eukaryote. It is known that T7 RNA polymerase produces abortive transcripts up to eight ribonucleotides in length depending on the initial sequence of the DNA message. On the other hand, T7 RNA polymerase initiates DNA replicat...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF00160407
更新日期：1994-12-01 00:00:00
abstract：:Previously we suggested that four proteins including aldolase and triose phosphate isomerase (TPI) evolved with approximately constant rates over long periods covering the whole animal phyla. The constant rates of aldolase and TPI evolution were reexamined based on three different models for estimating evolutionary di...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006208
更新日期：1997-07-01 00:00:00
abstract：:Here we report DNA sequences from mitochondrial cytochrome b gene segments (1,005 base pairs per species) for the extinct woolly mammoth (Mammuthus primigenius) and Steller's sea cow (Hydrodamalis gigas) and the extant Asian elephant (Elephas maximus), the Western Indian manatee (Trichechus manatus), and the hyrax (Pr...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/pl00006160
更新日期：1997-04-01 00:00:00
abstract：:Two competing effects at two vastly different scales may explain collagen's current translation length. The necessity to have long molecules for maintaining mechanical integrity at the organism and supraorganism scales may be limited by the need to have small molecules capable of robust self-assembly at the nanoscale....
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-008-9111-7
更新日期：2008-06-01 00:00:00
abstract：:Langley and Fitch (1974, 1976) have shown that the pattern of nucleotide substitutions in proteins is inconsistent with a Poisson process with constant rate. From this they conclude that the rate is temporally heterogeneous. It is pointed out in this note that a process which is temporally homogeneous but not a Poisso...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01732751
更新日期：1979-06-08 00:00:00
abstract：:The periodic protein collagen is of special interest for the study of the relationship which exists between the structure of a protein and that of its mRNA, because oligopeptides containing glycine, proline (hydroxyproline) and alanine occur with great frequency in it. Collagen is particularly rich in these amino acid...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/BF01739101
更新日期：1976-08-03 00:00:00
abstract：:Compared with the X chromosome, the mammalian Y chromosome is considerably diminished in size and has lost most of its ancestral genes during evolution. Interestingly, for the X-degenerate region on the Y chromosome, human has retained all 16 genes, while chimpanzee has lost 4 of the 16 genes since the divergence of t...
journal_title：Journal of molecular evolution
pub_type： 杂志文章
doi：10.1007/s00239-008-9189-y
更新日期：2009-02-01 00:00:00
