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  • 1
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    Seawater carbonate chemistry in experiment 1 and 2 (2022)
    PANGAEA
    Details
    Publication Date: 2024-03-15
    Description: Acidification-induced changes in neurological function have been documented in several tropical marine fishes. Here, we investigate whether similar patterns of neurological impacts are observed in a temperate Pacific fish that naturally experiences regular and often large shifts in environmental pH/pCO2. In two laboratory experiments, we tested the effect of acidification, as well as pH/pCO2 variability, on gene expression in the brain tissue of a common temperate kelp forest/estuarine fish, Embiotoca jacksoni. Experiment 1 employed static pH treatments (target pH = 7.85/7.30), while Experiment 2 incorporated two variable treatments that oscillated around corresponding static treatments with the same mean (target pH = 7.85/7.70) in an eight-day cycle (amplitude ± 0.15). We found that patterns of global gene expression differed across pH level treatments. Additionally, we identified differential expression of specific genes and enrichment of specific gene sets (GSEA) in comparisons of static pH treatments and in comparisons of static and variable pH treatments of the same mean pH. Importantly, we found that pH/pCO2 variability decreased the number of differentially expressed genes detected between high and low pH treatments, and that inter-individual variability in gene expression was greater in variable treatments than static treatments. These results provide important confirmation of neurological impacts of acidification in a temperate fish species and, critically, that natural environmental variability may mediate the impacts of ocean acidification.
    Keywords: Alkalinity, total; Alkalinity, total, standard deviation; Animalia; Aragonite saturation state; Aragonite saturation state, standard deviation; Bicarbonate ion; Bicarbonate ion, standard deviation; Calcite saturation state; Calcite saturation state, standard deviation; Calculated using seacarb after Nisumaa et al. (2010); Calculated using seacarb after Orr et al. (2018); Carbon, inorganic, dissolved; Carbon, inorganic, dissolved, standard deviation; Carbonate ion; Carbonate ion, standard deviation; Carbonate system computation flag; Carbon dioxide; Carbon dioxide, standard deviation; Chordata; Coast and continental shelf; Containers and aquaria (20-1000 L or 〈 1 m**2); Embiotoca jacksoni; Experiment; Fugacity of carbon dioxide (water) at sea surface temperature (wet air); Fugacity of carbon dioxide in seawater, standard deviation; Gene expression (incl. proteomics); Laboratory experiment; Nekton; North Pacific; OA-ICC; Ocean Acidification International Coordination Centre; Other; Partial pressure of carbon dioxide, standard deviation; Partial pressure of carbon dioxide (water) at sea surface temperature (wet air); Pelagos; pH; pH, standard deviation; Salinity; Salinity, standard deviation; Single species; Species, unique identification; Species, unique identification (Semantic URI); Species, unique identification (URI); Temperate; Temperature, water; Temperature, water, standard deviation; Treatment; Type
    Type: Dataset
    Format: text/tab-separated-values, 245 data points
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    DATA PANGAEA
  • 2
    Electronic Resource
    Electronic Resource
    Codon usage and genome composition (1985)
    Springer
    Journal of molecular evolution 22 (1985), S. 363-365 
    Details
    ISSN: 1432-1432
    Keywords: Codon usage ; Genome composition ; Coding sequences
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The GC levels of codon third positions from 49 genomes coveering a wide phylogenetic range are linearly correlated with the GC levels of the corresponding genomes. Three different relationships have been found: one for prokaryotes and viruses, one for lower eukaryotes, and one for vertebrates. All points not fitting the first relationship can be brought into quasi coincidence with it when plotted against GC levels of coding sequences.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02115693
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  • 3
    Electronic Resource
    Electronic Resource
    Specific compositional patterns of synonymous positions in homologous mammalian genes (1995)
    Springer
    Journal of molecular evolution 40 (1995), S. 293-307 
    Details
    ISSN: 1432-1432
    Keywords: Homologous mammalian genes ; Compositional patterns ; Synonymous positions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract All 69 homologous coding sequences that are currently available in four mammalian orders were aligned and the synonymous (ie., third) positions of quartet (fourfold degenerate) codons were divided into three classes (that will be called conserved, intermediate, and variable), according to whether they show no change, one change, and more than one change, respectively. The three classes were analyzed in their compositional patterns. In the majority of GC-rich genes, the three classes of positions (but especially conserved positions) exhibited significantly different base compositions compared to expectations based on a “random” substitution process from the “ancestral” (consensus) sequence to the present-day (actual) sequences. Significant differences were rare in GC-poor genes. An analysis of the present results indicates that natural selection plays a role in the synonymous nucleotide substitution process, especially in GC-rich genes which represent the vast majority of mammalian genes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00163234
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  • 4
    Electronic Resource
    Electronic Resource
    Compositional patterns in vertebrate genomes: Conservation and change in evolution (1988)
    Springer
    Journal of molecular evolution 28 (1988), S. 7-18 
    Details
    ISSN: 1432-1432
    Keywords: Compositional patterns ; Compositional shifts ; Genome evolution ; Isochores ; Vertebrates ; Selection ; Neutral theory
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The evolution of vertebrate genomes can be investigated by analyzing their regional compositional patterns, namely the compositional distributions of large DNA fragments (in the 30–100-kb size range), of coding sequences, and of their different codon positions. This approach has shown the existence of two evolutionary modes. In the conservative mode, compositional patterns are maintained over long times (many million years), in spite of the accumulation of enormous numbers of base substitutions. In the transitional, or shifting, mode, compositional patterns change into new ones over much shorter times. The conservation of compositional patterns, which has been investigated in mammalian genomes, appears to be due in part to some measure of compositional conservation in the base substitution process, and in part to negative selection acting at regional (isochore) levels in the genome and eliminating deviations from a narrow range of values, presumably corresponding to optimal functional properties. On the other hand, shifts of compositional patterns, such as those that occurred between cold-blooded and warm-blooded vertebrates, appear to be due essentially to both negative and positive selection again operating at the isochore level, largely under the influence of changes in environmental conditions, and possibly taking advantage of mutational biases in the replication/repair enzymes and/or in the enzyme make-up of nucleotide precursor pools. Other events (like translocations and changes in chromosomal structure) also play a role in the transitional mode of genome evolution. The present findings (1) indicate that isochores, which correspond to the DNA segments of individual or contiguous chromatin domains, represent selection units in the vertebrate genome; and (2) shed new light on the selectionist-neutralist controversy.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02143493
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  • 5
    Electronic Resource
    Electronic Resource
    Compositional constraints and genome evolution (1986)
    Springer
    Journal of molecular evolution 24 (1986), S. 1-11 
    Details
    ISSN: 1432-1432
    Keywords: Genome composition ; Isochores ; Neutral theory ; Natural selection
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary Nucleotide sequences of all genomes are subject to compositional constraints that (1) affect, to about the same extent, both coding and noncoding sequences; (2) influence not only the structure and function of the genome, but also those of transcripts and proteins; (3) are the result of environmental pressures; and (4) largely control the fixation of mutations. These findings indicate (1) that noncoding sequences are associated with biological functions; (2) that the organismal phenotype comprises two components, the classical phenotype, corresponding to the “gene products,” and a “genome phenotype,” which is defined by the compositional constraints; and (3) that natural selection plays a more important role in genome evolution than do random events.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02099946
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  • 6
    Electronic Resource
    Electronic Resource
    Compositional patterns in the nuclear genome of cold-blooded vertebrates (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 265-281 
    Details
    ISSN: 1432-1432
    Keywords: Genome ; Isochores ; Fishes ; Amphibians ; Reptiles
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary DNA preparations obtained from 122 species of fishes, 5 species of amphibians, and 13 species of reptiles were investigated in their compositional properties by analytical equilibrium centrifugation in CsCl density gradients. These species represented 21 orders of Osteichthyes, 3 orders of Chondrichthyes, 2 orders of amphibians, and 3 orders of reptiles. Modal buoyant densities of fish DNAs ranged from 1.696 to 1.707 g/cm3, the vast majority of values falling, however, between 1.699 and 1.704 g/cm3, which is the range covered by the DNAs of amphibians and reptiles. In all cases, DNA bands in CsCl were only weakly asymmetrical and only very rarely were accompanied by separate satellite bands (mostly on the GC-rich side). Intermolecular compositional heterogeneities were low in the vast majority of cases, and, like CsCl band asymmetries, at least partially due to cryptic or poorly resolved satellites. The present findings indicate, therefore, that DNAs from cold-blooded vertebrates are characterized by a number of common properties, namely a very wide spectrum of modal buoyant densities, low intermolecular compositional heterogeneities, low CsCl band asymmetries, and, in most cases, small amounts of satellite DNAs. In the case of fish DNAs a negative correlation was found between the GC level and the haploid size (c value) of the genome. If polyploidization is neglected, this phenomenon appears to be mainly due to the fact that increases and decreases in GC are associated with contraction and expansion phenomena, respectively, of intergenic noncoding sequences, which are GC poor relative to coding sequences.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02101122
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  • 7
    Electronic Resource
    Electronic Resource
    Compositional transitions in the nuclear genomes of cold-blooded vertebrates (1990)
    Springer
    Journal of molecular evolution 31 (1990), S. 282-293 
    Details
    ISSN: 1432-1432
    Keywords: Genome ; Isochores ; Vertebrates ; Directional mutations
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The compositional properties of DNAs from 122 species of fishes and from 18 other coldblooded vertebrates (amphibians and reptiles) were compared with those from 10 warm-blooded vertebrates (mammals and birds) and found to be substantially different. Indeed, DNAs from cold-blooded vertebrates are characterized by much lower intermolecular compositional heterogeneities and CsCl band asymmetries, by a much wider spectrum of modal buoyant densities in CsCl, by generally lower amounts of satellites, as well as by the fact that in no case do buoyant densities reach the high values found in the GC-richest components of DNAs from warm-blooded vertebrates. In the case of fish genomes, which were more extensively studied, different orders were generally characterized by modal buoyant densities that were different in average values as well as in their ranges. In contrast, different families within any given order were more often characterized by narrow ranges of modal buoyant densities, and no difference in modal buoyant density was found within any single genus (except for the genusAphyosemion, which should be split into several genera). The compositional differences that were found among species belonging to different orders and to different families within the same order are indicative of compositional transitions, which were shown to be essentially due to directional base substitutions. These transitions were found to be independent of geological time. Moreover, the rates of directional base substitutions were found to be very variable and to reach, in some cases, extremely high values, that were even higher than those of silent substitutions in primates. The taxonomic and evolutionary implications of these findings are discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02101123
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  • 8
    Electronic Resource
    Electronic Resource
    Compositional properties of nuclear genes from cold-blooded vertebrates (1991)
    Springer
    Journal of molecular evolution 33 (1991), S. 57-67 
    Details
    ISSN: 1432-1432
    Keywords: Genomes ; Genes ; Base composition ; Vertebrates
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have investigated the compositional properties of coding sequences from cold-blooded vertebrates and we have compared them with those from warm-blooded vertebrates. Moreover, we have studied the compositional correlations of coding sequences with the genomes in which they are contained, as well as the compositional correlations among the codon positions of the genes analyzed. The distribution of GC levels of the third codon positions of genes from cold-blooded vertebrates are distinctly different from those of warm-blooded vertebrates in that they do not reach the high values attained by the latter. Moreover, coding sequences from cold-blooded vertebrates are either equal, or, in most cases, lower in GC (not only in third, but also in first and second codon positions) than homologous coding sequences from warm-blooded vertebrates; higher values are exceptional. These results at the gene level are in agreement with the compositional differences between cold-blooded and warm-blooded vertebrates previously found at the whole genome (DNA) level (Bernardi and Bernardi 1990a,b). Two linear correlations were found: one between the GC levels of coding sequences (or of their third codon positions) and the GC levels of the genomes of cold-blooded vertebrates containing them; and another between the GC levels of third and first+ second codon positions of genes from cold-blooded vertebrates. The first correlation applies to the genomes (or genome compartments) of all vertebrates and the second to the genes of all living organisms. These correlations are tantamount to a genomic code.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02100196
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  • 9
    Electronic Resource
    Electronic Resource
    Molecular phylogeny of bony fishes, based on the amino acid sequence of the growth hormone (1993)
    Springer
    Journal of molecular evolution 37 (1993), S. 644-649 
    Details
    ISSN: 1432-1432
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Bony fishes (Osteichthyes) comprise over 22,000 species, about half of all vertebrate species. In order to investigate the phylogenetic relationships within this vertebrate class, we have studied the only protein whose primary structure is known in a rather large (27) number of fish species belonging to seven orders—the growth hormone. The phylogeny obtained using the maximum parsimony method based on amino acid sequences represents the first molecular phylogeny of teleostean fishes based on an extensive set of data. This phylogeny agrees remarkably well with the generally accepted phylogeny based on morphological characters and paleontological data.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00182750
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  • 10
    Electronic Resource
    Electronic Resource
    Chromosome banding and genome compartmentalization in fishes (1988)
    Springer
    Chromosoma 96 (1988), S. 178-183 
    Details
    ISSN: 1432-0886
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Notes: Abstract We have investigated the correlation between chromosome banding and compositional compartmentalization of the genome in three selected fish species, Anguilla anguilla (Anguilliformes), Epinephelus guttatus (Perciformes), and Labeo bicolor (Cypriniformes). These species were selected because they provided a spectrum of such compartmentalizations. Indeed, the band profiles in CsCl density gradients of the corresponding DNAs are characterized by a high compositional heterogeneity and a strong asymmetry for A. anguilla and by a very low compositional heterogeneity and a very weak asymmetry for E. guttatus. L. bicolor DNA shows an intermediate situation. — Chromosomes were studied using three consecutive stainings of the same mitoses. The intensity and reciprocity of the patterns obtained after Q- and R-banding were relatively strong for A. anguilla, whereas essentially no banding was found for E. guttatus. L. bicolor exhibited a chromosome banding of intermediate intensity and reciprocity. There is therefore a parallelism between chromosome banding and compositional compartmentalization of the genome. This finding provides new, independent support for previous indications of a correlation between these two properties.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00331050
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