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PubMed2003

Evolutionary history of asexual hybrid loaches (Cobitis: Teleostei) inferred from phylogenetic analysis of mitochondrial DNA variation.

Reconstruction of the evolutionary history of asexual lineages undermines their suitability as models for the studies of evolutionary consequences of sexual reproduction. Using molecular tools we addressed the origin, age and maternal ancestry of diploid and triploid asexual lineages arisen through the hybridization between spiny loaches Cobitis elongatoides, C. taenia and C. tanaitica. Reconstructions of the phylogenetic relationships among mitochondrial DNA (mtDNA) haplotypes, revealed by sequence analyses, suggest that both hybrid complexes (C. elongatoides-taenia and C. elongatoides-tanaitica) contained several asexual lineages of independent origin. Cobitis elongatoides was the exclusive maternal ancestor of all the C. elongatoides-tanaitica hybrids, whereas within the C. elongatoides-taenia complex, hybridization was reciprocal. In both complexes the low haplotype divergences were consistent with a recent origin of asexual lineages. Combined mtDNA and allozyme data suggest that the triploids arose through the incorporation of a haploid sperm genome into unreduced ova produced by diploid hybrids.

Animals↗
PubMed2002

Multispecies comparison of the casein gene loci and evolution of casein gene family.

Caseins, the major milk proteins, are present in a genomic cluster spanning 250-350 kb. The divergence at the coding level between human, rodent, and cattle sequences is rather extensive for most of the genes in this region. Nevertheless, comparative analysis of genomic sequences harboring the casein gene cluster region of these species (with equal evolutionary distances 79-88 Myr) shows that the organization and orientation of the genes is highly conserved. The conserved gene structure indicates that the molecular diversity of the casein genes is achieved through variable use of exons in different species and high evolutionary divergence. Comparative analysis also revealed the presence within two species of uncharacterized casein family members and ruled out the previously held notion that another gene family, located in this region, is primate-specific. Several other new genes as well as conserved noncoding sequences with potential regulatory functions were identified. All genes identified in this region are, or are predicted to be, secreted proteins involved in mineral homeostasis, nutrition, and/or host defense, and are mostly expressed in the mammary and/or salivary glands. These observations suggest a possible common ancestry for the genes in this region.

Amino Acid Sequence↗
PubMedDate not supplied

The art of nursing: a concept analysis.

That nursing is a science and an art is commonly accepted. While much emphasis has been placed on the science in nursing, the art of nursing is less well-understood. A concept analysis using Rodgers' evolutionary perspective was conducted to examine the meaning of the art of nursing. Through the analysis, a definition emerged suggesting that the art of nursing is the intentional creative use of oneself, based upon skill and expertise, to transmit emotion and meaning to another. It is a process that is subjective and requires interpretation, sensitivity, imagination, and active participation.

Creativity↗
PubMed1995

Control analysis of transit time for free and enzyme-bound metabolites: physiological and evolutionary significance of metabolic response times.

Control analysis of transit time, defined as tau = delta/J, has previously been considered with the constraint of low enzyme concentrations compared with free pools of metabolites [Meléndez-Hevia, Torres, Sicilia and Kacser (1990) Biochem. J. 265, 195-202]. One of the conclusions was that the sum of the control coefficients of the transition time with respect to enzyme concentration was -1. Here we demonstrate that, if the enzyme-bound pools are taken into consideration (which would be important at high enzyme concentrations and high affinities), the sum lies between 0 and -1. The transition time between two steady states, which are frequent physiological events, is mainly governed by time constants involved in changing the enzyme concentrations. Some physiological and evolutionary aspects are discussed.

Enzymes↗
PubMed2005

Evolutionary regulation of the blind subterranean mole rat, Spalax, revealed by genome-wide gene expression.

We applied genome-wide gene expression analysis to the evolutionary processes of adaptive speciation of the Israeli blind subterranean mole rats of the Spalax ehrenbergi superspecies. The four Israeli allospecies climatically and adaptively radiated into the cooler, mesic northern domain (N) and warmer, xeric southern domain (S). The kidney and brain mRNAs of two N and two S animals were examined through cross-species hybridizations with two types of Affymetrix arrays (mouse and rat) and muscle mRNA of six N and six S animals with spotted cDNA mouse arrays. The initial microarray analysis was hypothesis-free, i.e., conducted without reference to the origin of animals. Principal component analysis revealed that 20-30% of the expression signal variability could be explained by the differentiation of N-S species. Similar N-S effects were obtained for all tissues and types of arrays: two Affymetrix microarrays using probe oligomer signals and the spotted array. Likewise, ANOVA and t test statistics demonstrated significant N-S ecogeographic divergence and region-tissue specificity in gene expression. Analysis of differential gene expression between species corroborates previous results deduced by allozymes and DNA molecular polymorphisms. Functional categories show significant N-S ecologic putative adaptive divergent up-regulation of genes highlighting a higher metabolism in N, and potential adaptive brain activity and kidney urine cycle pathways in S. The present results confirm ecologic-genomic separation of blind mole rats into N and S. Gene expression regulation appears to be central to the evolution of blind mole rats.

Adaptation, Physiological↗
PubMed2003

Broad-scale analysis contradicts the theory that generation time affects molecular evolutionary rates in plants.

Several studies of plant taxa have concluded that generation time, including annual/perennial life history, may explain molecular evolutionary rate variation in selectively neutral DNA. Unlike in animals, there is little theoretical basis for why generation-time effects would exist in plants. Furthermore, previous reports fail to establish the generality of a generation-time effect in plants because of the small size of the datasets, a large proportion of which compared very widely divergent taxa differing in many characteristics other than generation time. Using 24 phylogenetically independent species pairs, each containing a species with an annual and a species with a perennial life history, and nine species pairs, each containing a tree species with a short and a long minimum generation time, we found no evidence that generation time is related to molecular evolutionary rate variation of the nuclear 18S ITS1 and ITS2 regions. This analysis strongly contradicts the growing belief that evolutionary rates are affected by generation time in plants. Possible reasons for the absence of generation-time effects are discussed, including an evaluation of the cell-division theory.

DNA, Intergenic↗
PubMed2002

Gene organization and expression of a neuropeptide Y homolog from the land planarian Arthurdendyus triangulatus.

Neuropeptide Y is one of the most widespread regulatory peptides within the vertebrate nervous system and shares the C-terminal motif [FY]-x(3)-[LIVM]-x(2)-Y-x(3)-[LIVMFY]-x-R-x-R-[YF] with pancreatic polypeptide, peptide YY, and fish pancreatic peptide Y. All four peptides are believed to have arisen from a single ancestral gene through successive gene duplication events in vertebrates. The origin of this peptide family may date back further still; similarly sized peptide transmitters with an identical C-terminal motif have been identified in molluscs and flatworms and designated neuropeptide F (NPF). Cloning of the npf gene from the parasitic flatworm Moniezia expansa identified some unusual features within the peptide precursor organization but, at the same time, provided support for an evolutionary relationship of npf and npy genes through the presence of a single intron at a conserved position. To extend the analysis of the evolutionary relationships between invertebrate NPF and vertebrate NPY family peptides, the NPF precursor from the turbellarian Arthurdendyus triangulatus was characterized. Sequence analysis revealed the npf transcript to be 362 base pairs in length encoding a single open reading frame of 81 amino acids. The precursor comprises a signal peptide followed by the mature peptide of 36 amino acids in length, terminating in the typical invertebrate GRPRF motif, followed by a carboxyterminal glycyl extension. The NPF precursor of A. triangulatus shows significant similarities to the vertebrate NPY peptides. Indeed, the N-terminus of A. triangulatus prepro-NPF corresponds more closely to that of the vertebrate peptide homologs than to that of other invertebrate NPFs isolated to date. Immunocytochemical localization studies have demonstrated NPF immunoreactivity throughout the nervous system of A. triangulatus, particularly in association with muscular structures. The data support an early evolutionary origin for this peptide transmitter family within the nervous system of basal bilaterians.

Amino Acid Sequence↗
PubMed2001

Bayesian inference of phylogeny and its impact on evolutionary biology.

As a discipline, phylogenetics is becoming transformed by a flood of molecular data. These data allow broad questions to be asked about the history of life, but also present difficult statistical and computational problems. Bayesian inference of phylogeny brings a new perspective to a number of outstanding issues in evolutionary biology, including the analysis of large phylogenetic trees and complex evolutionary models and the detection of the footprint of natural selection in DNA sequences.

Algorithms↗
PubMed2006

Molecular evolution and population genetic analysis of candidate female reproductive genes in Drosophila.

Molecular analyses in several taxa have consistently shown that genes involved in reproduction are rapidly evolving and subjected to positive selection. The mechanism behind this evolution is not clear, but several proposed hypotheses involve the coevolution between males and females. In Drosophila, several male reproductive proteins (Acps) involved in male-male and male-female interactions show evidence of rapid adaptive evolution. What has been missing from the Drosophila literature is the identification and analysis of female reproductive genes. Recently, an evolutionary expressed sequence tag analysis of Drosophila female reproductive tract genes identified 169 candidate female reproductive genes. Many of these candidate genes still await further molecular analysis and independent verification of positive selection. Our goal was to expand our understanding of the molecular evolution of Drosophila female reproductive genes with a detailed polymorphism and divergence study on seven additional candidate female reproductive genes and a reanalysis of two genes from the above study. We demonstrate that 6 candidate female genes of the 9 genes surveyed show evidence of positive selection using both polymorphism and divergence data. One of these proteins (CG17012) is modeled to reveal that the sites under selection fall around and within the active site of this protease, suggesting potential differences between species. We discuss our results in light of potential function as well as interaction with male reproductive proteins.

Animals↗
PubMed2005

Carotenoid biosynthetic pathway: molecular phylogenies and evolutionary behavior of crt genes in eubacteria.

Phylogenetic analysis of carotenoid biosynthetic pathway genes and their evolutionary rate variations were studied among eubacterial taxa. The gene sequences for the enzymes involved in this pathway were obtained for major phylogenetic groups of eubacteria (green sulfur bacteria, green nonsulphur bacteria, Gram-positive bacteria, proteobacteria, flavobacteria, cyanobacteria) and archeabacteria. These gene datasets were distributed under five major steps of carotenoid biosynthesis in eubacteria; isoprenoid precursor biosynthesis, phytoene synthesis, dehydrogenation of phytoene, lycopene cyclization, formation of acyclic xanthophylls, formation of cyclic xanthophylls and carotenoid biosynthesis regulation. The NJ algorithm was used on protein coding DNA sequences to deduce the evolutionary relationship for the respective crt genes among different eubacterial lineages. The rate of nonsynonymous nucleotide substitutions per nonsynonymous site (d(N)) and synonymous nucleotide substitutions per synonymous site (d(S)) were calculated for different clades of the respective phylogenetic tree for specific crt genes. The phylogenetic analysis suggests that evolutionary pattern of crt genes in eubacteria is characterized by lateral gene transfer and gene duplication events. The d(N) values indicate that carotenoid biosynthetic genes are more conserved in proteobacteria than in any other eubacterial phyla. Furthermore, of the genes involved in carotenoid biosynthesis pathway, structural genes evolve slowly than the regulatory genes in eubacteria.

Bacteria↗
PubMed1988

Comparative chemical anatomy of the brain: concepts and methods.

The study of neuropeptides represents an appropriate playground for comparative and evolutionary research. Comparative analysis can give insight into the conservative pattern of intercellular transmission molecules, possibly bound both to some evolutionary antiquity and to cellular constraints. In the same time it can teach us how modulation has occurred at molecular, cellular, multicellular levels in order to give the species-specific functional organization. Using some examples from vertebrate central neurons system (CNS) immunocytochemical analyses, the results so far obtained suggest the rise of a new comparative chemical neuroanatomy. The rationale of "what" and "why" we are comparing is, however, needed in order to understand constancy, heterogeneity or else trends toward complexity in the distribution of neuropeptides.

Anatomy, Comparative↗
PubMed2000

Evidence for evolutionary stasis and genetic drift by genetic analysis of two equine influenza H3 viruses isolated in France.

The amino acid sequences of the HA(1) portion of the haemagglutinin of two equine A(H3N8) influenza viruses isolated in France in 1993 and 1998 were analysed to determine their evolutionary relationship with 51 other HA(1) amino acid sequences available in databanks. Our data show that the French strain isolated in 1993 belongs to a group of phylogenetically related viruses branched on the main trunk, illustrating the main lineage of evolution of the equine-2 H3 sequences before its split into two distinct lineages in the late 1980s. By contrast, the 1998 French isolate appears to belong to the more recent 'Eurasian' lineage. These data suggest that equine-2 strains antigenically related to old prototype viruses may cocirculate with the more recent 'Eurasian' and 'American' lineages. In conclusion, it may be necessary to include both strains representative of recent equine influenza variants and an older prototype strain in the current equine influenza vaccines.

Amino Acid Sequence↗
PubMed2002

The evolutionary history of prosaposin: two successive tandem-duplication events gave rise to the four saposin domains in vertebrates.

Prosaposin is a multifunctional protein encoded by a single-copy gene. It contains four saposin domains (A, B, C, and D) occurring as tandem repeats connected by linker sequences. Because the saposin domains are similar to one another, it is deduced that they were created by sequential duplications of an ancestral domain. There are two types of evolutionary scenarios that may explain the creation of the four-domain gene: (1) two rounds of tandem internal gene duplication and (2) three rounds of duplications. An evolutionary and phylogenetic analysis of saposin DNA and amino acid sequences from human, mouse, rat, chicken, and zebrafish indicates that the first evolutionary scenario is the most likely. Accordingly, an ancestral saposin-unit duplication produced a two-domain gene, which, subsequently, underwent a second complete tandem duplication to give rise to the present four-domain structure of the prosaposin gene.

Amino Acid Sequence↗
PubMed1999

Partial nucleotide sequencing and molecular evolution of epidemic causing Dengue 2 strains.

To study the genetic variability and to detect evolutionary changes and movement of dengue 2 (DEN-2) strains, nucleotide sequencing of the envelope protein gene and the nonstructural protein 1 gene junction was performed for 9 isolates from the 1996 Delhi epidemic and 1 isolate from the 1967 Delhi epidemic. The epidemic strains had a divergence of 10%-11% from the 1967 strains, but were quite similar to DEN-2 isolates from Seychelles, Somalia, and Torres Strait. In addition, the sequence data were compared to the prototype DEN-2 strain, New Guinea C, and other published DEN-2 sequences from different parts of the world. The phylogenetic analysis by the Molecular Evolutionary Genetics Analysis program suggests that the 1996 Delhi isolates of DEN-2 were genotype IV. The 1967 isolate was similar to a 1957 isolate of DEN-2, P9-122, from India, and was classified as genotype V. This study indicates that earlier DEN-2 strains of genotype V have been replaced by genotype IV.

Base Sequence↗
PubMed1999

[Phylogenetic analysis based on groE shows the closest evolutionary relationship between mitochondria and Rickettsia].

The nucleotide sequence of the groE operon of Rickettsia prowazekii, the obligate intracellular parasite of eukaryotes, was determined. The alignment of DNA-inferred amino acid sequences of the Hsp10 and Hsp60 heat-shock proteins with bacterial and mitochondrial homologues revealed the presence within Hsp60 of signatures shared by mitochondria and rickettsiae. Phylogenetic analysis demonstrated that heat-shock proteins of R. prowazekii are the earliest and the least diverging homologues within the family Rickettsiaceae--a sister group to the monophyletic clade of mitochondria. These results are in good agreement with the data obtained when using other molecular chronometers and show the closest relationship between mitochondria and Rickettsia. The possible nature of obligate intracellular parasitism of rickettsiae has been considered on the basis of the assumption that they and mitochondria could have a common evolutionary origin.

Amino Acid Sequence↗
PubMed1996

Phylogenetic analysis of Metabacterium polyspora: clues to the evolutionary origin of daughter cell production in Epulopiscium species, the largest bacteria.

It is rare that there are molecular clues to the evolutionary origin of developmental traits. We have encountered an evolutionary juxtaposition that may explain the origin of the unique replicative morphology of Epulopiscium spp., the largest known bacteria, which reproduce by the internal production of multiple live offspring. We report here a 16S rRNA-based phylogenetic analysis of Metabacterium polyspora, a multiple-endospore-forming, uncultivated inhabitant of guinea pig cecum. Cells of M. polyspora were harvested from cecum contents by sedimentation in a Ficoll gradient and lysed. The bacterial 16S rRNA genes of this lysate were amplified by PCR. Sequence analysis of the cloned PCR products revealed two dominant, closely related 16S rRNA types. In situ hybridization of cecum contents with fluorescently labeled oligonucleotides, diagnostic of these two sequences, showed that they represent distinct strains of M. polyspora. Phylogenetic analyses of the sequences showed that M. polyspora is closely related to Epulopiscium spp. On the basis of this result and other correlations, we propose that the process of sporulation was modified in a predecessor of Epulopiscium spp. to produce live offspring instead of quiescent endospores.

Animals↗
PubMed2000

Genetics of adaptive radiation in Hawaiian species of Tetramolopium (Asteraceae). III. Evolutionary genetics of sex expression.

Despite numerous studies of speciation on oceanic islands, few insights exist on the genetic changes involved in the origin and diversification of island taxa. Here we report a genetic analysis of the evolutionary change in sex expression in Hawaiian Tetramolopium. The most diverse clade in the genus is characterized by a monoecious breeding system. The breeding system resulted from a change in sex expression in disc florets from the ancestral hermaphroditic condition to the derived male state. Analysis of an F2 population from a cross between the two forms of sex expression indicates two regions of the Tetramolopium linkage map are associated with the loss of female function in disc florets. Quantitative trait locus mapping of the two linkage groups confirms that two loci control 56% of the phenotypic variation of the trait in the F2 population. Additive and dominance effects are apparent but no statistical evidence of epistasis was found. Several related reproductive traits also have few genetic associations on the linkage map, but are generally distinct from the control of sex expression. Although modifier loci are likely to be involved, the apparent simple genetic change underlying sex expression parallels a major evolutionary diversification in Hawaiian Tetramolopium and may have initiated the divergence of this novel clade.

Adaptation, Biological↗
PubMed1994

Identification of functional domains in the plasma apolipoproteins by analysis of inter-species sequence variability.

Molecular evolution theory posits that sequence motifs essential for protein function are constrained by selective pressure from changing over long stretches of evolutionary time. Thus, analysis of inter-species amino acid sequence variability, by identifying highly conserved intervals, should predict the location of domains critical for protein function. We have analyzed the amino acid sequences of the mammalian apolipoproteins A-I, A-IV, C-I, C-II, C-III, D, and E with a computer algorithm that calculates numerical residue variability scores. The application of a median sieve filter to the data facilitated identification of the exact boundaries of highly conserved domains, which coincided with the location of known structural features and functional domains in this family of proteins. The analysis also identified highly conserved intervals in every apolipoprotein whose function is unknown at present, but which are candidates for regions with specific functional roles.

Amino Acid Sequence↗