Concerted evolution of repetitive DNA sequences in eukaryotes.

A large fraction, sometimes the largest fraction, of a eukaryotic genome consists of repeated DNA sequences. Copy numbers range from several thousand to millions per diploid genome. All classes of repetitive DNA sequences examined to date exhibit apparently general, but little studied, patterns of "concerted evolution." Historically, concerted evolution has been defined as the nonindependent evolution of repetitive DNA sequences, resulting in a sequence similarity of repeating units that is greater within than among species. This intraspecific homogenization of repetitive sequence arrays is said to take place via the poorly understood mechanisms of "molecular drive." The evolutionary population dynamics of molecular drive remains largely unstudied in natural populations, and thus the potential significance of these evolutionary dynamics for population differentiation is unknown. This review attempts to demonstrate the potential importance of the mechanisms responsible for concerted evolution in the differentiation of populations. It contends that any natural grouping that is characterized by reproductive isolation and limited gene flow is capable of exhibiting concerted evolution of repetitive DNA arrays. Such effects are known to occur in protein and RNA-coding repetitive sequences, as well as in so-called "junk DNA," and thus have important implications for the differentiation and discrimination of natural populations.

Extreme clonal uniformity of Phoxinus eos/neogaeus gynogens (pisces: Cyprinidae) among variable habitats in northern Minnesota beaver ponds.

Genetic surveys of parthenogenetic vertebrate populations have demonstrated a common pattern of relatively high degrees of clonal variation and the coexistence of numerous clones. In striking contrast, the Phoxinus eos/Phoxinus neogaeus/hybrid gynogen complex of cyprinid fishes exhibits no clonal variation within a northern Minnesota drainage characterized by successional beaver ponds. Gynogens were sampled from three habitats in each of four different pond types in a single drainage in Voyageurs National Park, Minnesota. The abundance of gynogens relative to sexual dace varied with pond type, being least common in deep upland ponds and most common in shallow, collapsed, lowland ponds (13.4% and 48.6%, respectively). Simple-sequence multilocus DNA fingerprinting of 464 individual gynogens detected one, and only one, clone. DNA fingerprints, generated sequentially by using three oligonucleotide probes, (CAC)5, (GACA)4, and the Jeffreys' 33.15 probe, all revealed the same unprecedented lack of variation. The extreme lack of clonal diversity in these gynogens across a range of habitat types does not fit the general pattern of high clonal diversity found within populations of other vertebrate parthenogens.

Concerted evolution at the population level: pupfish HindIII satellite DNA sequences.

The canonical monomers (approximately 170 bp) of an abundant (1.9 x 10(6) copies per diploid genome) satellite DNA sequence family in the genome of Cyprinodon variegatus, a "pupfish" that ranges along the Atlantic coast from Cape Cod to central Mexico, are divergent in base sequence in 10 of 12 samples collected from natural populations. The divergence involves substitutions, deletions, and insertions, is marked in scope (mean pairwise sequence similarity = 61.6%; range = 35-95.9%), is largely confined to the 3' half of the monomer, and is not correlated with the distance among collecting sites. Repetitive cloning and direct genomic sequencing experiments failed to detect intrapopulation and intraindividual variation, suggesting high levels of sequence homogeneity within populations. The satellite sequence has therefore undergone "concerted evolution," at the level of the local population. Concerted evolution has previously almost always been discussed in terms of the divergence of species or higher taxa; its intraspecific occurrence apparently has not been reported previously. The generality of the observation is difficult to evaluate, for although satellite DNAs from a large number of organisms have been studied in detail, there appear to be little or no other data on their sequence variation in natural populations. The relationship (if any) between concerted, population level, satellite DNA divergence and the extent of gene flow/genetic isolation among conspecific natural populations remains to be established.

Extreme clonal diversity and divergence in populations of a selfing hermaphroditic fish.

Recombination is unknown in natural populations of Rivulus marmoratus, a selfing hermaphrodite, and genetic variation is likely due to mutation alone. DNA fingerprinting with an array of microsatellite [e.g., (CT)9] and minisatellite (e.g., the 33.15 core sequence) probes reveals very high clonal diversity within samples of seven Floridian populations, of which five contain about as many clones as there are individuals. There are 42 clones among 58 individuals surveyed (mean, 1.4 individuals per clone), a level of genetic diversity unprecedented among clonal animals. Moreover, all of the probes recognize the same clones even though, at high hybridization stringencies, there is little overlap in the fingerprint patterns they generate. This suggests that most sympatric clones differ by multiple and independent mutational steps. In one population studied in detail, the average number of mutational steps separating two clones is estimated at 9 or 10 and may be substantially higher. The mutational discontinuities among sympatric clones make it unlikely that they evolved by accumulation of neutral mutations in populations that are otherwise genetically uniform. The data argue that the mixing of unrelated individuals from different local populations occurs to an extent previously unappreciated and/or that divergence of clones is mediated by natural selection. If confirmed, the latter would be a serious challenge to current ideas on the predominant role of recombination in promoting the evolution of biological novelty.

Freshwater molluscs as indicators of bioavailability and toxicity of metals in surface-water systems.

Freshwater molluscs--snails and bivalves--have been used frequently as bioindicator organisms. With increasing needs for research on contaminant effects in freshwater ecosystems, this kind of biomonitoring is likely to develop further in the future. Molluscs can be used effectively for studies of both organic and inorganic contaminants; this review focuses on studies involving bioaccumulation and toxicity of metals. Two important advantages of snails and bivalves over most other freshwater organisms for biomonitoring research are their large size and limited mobility. In addition, they are abundant in many types of freshwater environments and are relatively easy to collect and identify. At metal concentrations that are within ranges common to natural waters, they are generally effective bioaccumulators of metals. Biomonitoring studies with freshwater molluscs have covered a wide diversity of species, metals, and environments. The principal generalization that can be drawn from this research is that bioaccumulation and toxicity are extremely situation dependent; hence, it is difficult to extrapolate results from any particular study to other situations where the biological species or environmental conditions are different. Even within one species, individual characteristics such as size, life stage, sex, and genotype can have significant effects on responses to contaminants. The bioavailability of the metal is highly variable and depends on pH, presence of organic ligands, water hardness, and numerous other controlling factors. Despite this variability, past studies provide some general principles that can facilitate planning of research with freshwater snails and bivalves as metal bioindicators. These principles may also be useful in understanding and managing freshwater ecosystems. Bioaccumulation of metals in biota is a function of both uptake and depuration. Uptake in molluscs may be through either of two vectors--ingestion of food and other metal-containing substances or through direct adsorption of dissolved constituents. Under some conditions, the bioconcentration factors can be in the range of 10(3) to 10(6), relative to water. Most studies that provide comparisons among taxonomic groups indicate that bioaccumulation in molluscs is greater than that is fish. However, such comparisons should be interpreted with caution because metals tend to be nonuniformly distributed among different organs in both molluscs and fish. Bioaccumulation and acute and chronic toxicity are highly dependent on metal speciation. Mainly because of this influence of metal speciation, toxicity and bioaccumulation do not have a consistent relation to each other. Sensitivity to toxic effects of a metal is likely to be considerably greater in juvenile or larval stages than in adults.

Quantitative determination of selected compounds in a Kentucky 1R4F reference cigarette smoke by multidimensional gas chromatography and selected ion monitoring-mass spectrometry.

Eight compounds from a Kentucky 1R4F reference cigarette smoke condensate have been determined by selected ion monitoring-mass spectrometry (SIM-MS) to confirm the validity of multidimensional gas chromatography (MDGC) as a quantitative tool in complex mixture analyses. Four electrostatically precipitated smoke condensate samples of 100 cigarettes each are dissolved individually in 25 mL of 2-propanol. The 2-propanol contains two methyl esters (C8 and C14) and seven deuterium-labeled compounds used as internal standards (IS). Analysis of the compounds of interest, pyridine; acetamide; acrylamide; phenol; o-, m-, and p-cresol; and quinoline, is accomplished by using two heartcuts. Heartcut times of the MDGC analysis are selected such that at least one IS is transferred with each group of compounds being analyzed. This study shows that the MDGC technique previously developed and described can be used for quantitative analyses. A comparison is made between the two types of internal standards. The results obtained for both types of internal standards agree within 20% of each other, on the average, with higher standard deviations for approximately 60% of the compounds where methyl esters are used as internal standards.

Genetic variation in clonal vertebrates detected by simple-sequence DNA fingerprinting.

The measurement of clonal heterogeneity is central to understanding the evolutionary and population genetics of the roughly 50 species of vertebrates that lack effective genetic recombination. Simple-sequence DNA fingerprinting with oligonucleotide probes (CAC)5 and (GACA)4 is a sensitive and efficient means of detecting this heterogeneity in natural populations of two clonal fishes, Poecilia formosa, an apomictic unisexual, and Rivulus marmoratus, a selfing hermaphrodite. The fingerprints are clonally stable for at least three generations. The technique clearly differentiates allozymically identical laboratory lines of R. marmoratus that were previously distinguishable only by histocompatibility analysis. The technique also reveals apparent cases of shifts in clonal composition of a natural population of each species. Clonal variation in most natural populations is quite high. For example, a sample of 19 specimens of P. formosa from one station on the Rio Soto la Marina contained 16 clones (average clonal frequency = 0.07). This level of clonal diversity implies that mutation, subsequent to the founding of clonal lineages, is an important source of variation in these populations. It also suggests that chance (sampling error) has a previously unappreciated role in determining the clonal composition of populations even though some of the clones may be divergent in biologically significant features.

Analysis of flue-cured tobacco essential oil by hyphenated analytical techniques.

The major components of an alkaloid-free, flue-cured, tobacco essential oil sample are isolated and identified. This is accomplished by utilizing modern hyphenated analytical methods. The instrumentation developed to accomplish this are an automated multidimensional gas chromatograph/mass spectrometer/flame ionization detector (MDGC/MS/FID) and a multidimensional gas chromatograph/matrix isolation/Fourier transform infrared spectrometer (MDGC/MI/FTIR). A total of 306 compounds is identified in the essential oil, of which 80 are found as tobacco constituents for the first time.

Accumulation and bioconcentration of polycyclic aromatic hydrocarbons in a nearshore estuarine environment near a Pensacola (Florida) creosote contamination site.

Long-term accumulation of creosote wastes at a wood-preserving facility near Pensacola, Florida, has produced high levels of organic contamination of groundwaters near Pensacola Bay. Impacts of this contamination on the nearshore environment of the bay were examined by analysis of water, sediment and tissues of two mollusc species. One of the species (Thais haemastoma) was native to the study area. Individuals of the other test species (Crassostrea virginica) were placed in cages at the test sites for a 6-week period. Contamination at the nearshore estuarine sites was assessed by comparison to a control site in an uncontaminated area of the bay, as well as a small stream which forms a direct surface-water link between the creosote storage ponds and the bay. The study focused on polycyclic aromatic hydrocarbons (PAH), the primary components of creosote. Very little PAH in water or in the surface layer of estuarine sediments was detected, despite heavy pollution of the stream sediments. This is attributed to various degradation processes which attack the PAH compounds once they discharge into the estuary, and to the likelihood of intermittent and localised release of contaminants to the estuary. Examination of sediment cores and mollusc tissues, which provide a record integrated over time and space, revealed some accumulation of a few PAH, notably fluoranthene, pyrene, benzo(a)anthracene, chrysene and phenanthrene. In the sediments, the highest concentrations of these compounds appeared below the surface, within a depth range of 8-13 cm. Bioaccumulation of fluoranthene, pyrene and phenanthrene in both mollusc species was up to ten times greater at test sites than at the control site. This contrasts with naphthalene, the bioaccumulation of which was no greater at test sites than at the control site. These differences in bioaccumulation factors relate to structural chemistry of the compounds which control their solubility, bioavailability, susceptibility to degradation and capacity for depuration by the organism.