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PubMed2006

Population bottlenecks in quasispecies dynamics.

The characteristics of natural populations result from different stochastic and deterministic processes that include reproduction with error, selection, and genetic drift. In particular, population fluctuations constitute a stochastic process that may play a very relevant role in shaping the structure of populations. For example, it is expected that small asexual populations will accumulate mutations at a higher rate than larger ones. As a consequence, in any population the fixation of mutations is accelerated when environmental conditions cause population bottlenecks. Bottlenecks have been relatively frequent in the history of life and it is generally accepted that they are highly relevant for speciation. Although population bottlenecks can occur in any species, their effects are more noticeable in organisms that form large and heterogeneous populations, such as RNA viral quasispecies. Bottlenecks can also positively select and isolate particles that still keep the ability to infect cells from a disorganized population created by crossing the error threshold.

Base Sequence↗

PubMed1994

Metal speciation by supercritical fluid extraction with on-line detection by atomic absorption spectrometry.

A silica flame-in-tube interface is described for the sensitive detection, by AAS, of As, Cd, Cu, Mn, Pb, Se, or Zn in supercritical (SC) fluid extractor eluate. In operation, analyte metal in aqueous medium is derivatized by in situ complexation with tetrabutylammonium dibutyldithiocarbamate (TBADB-DTC) and the product complex is mobilized into SC-CO2. The extraction process is equally efficient whether the mobile phase is presaturated with complexing agent during a static preequilibration stage of the process or this reagent is solubilized dynamically as the mobile phase traverses a saturation vessel placed in series with the extraction vessel. SC-CO2 extractor eluate is nebulized into a diffused flame maintained within the upper region of the flame tube and the optical tube of the interface. Optimal flame conditions maintained with separate flows of O2 and H2 to the base of the flame tube are slightly reducing for aqueous and SC-CO2 mobile phases but slightly oxidizing for a methanolic mobile phase. For each analyte element, limits of detection were subnanogram to low picogram if standard was flow injected into the mobile phase. These sensitivities permitted differences in the rates of mobilization of analyte metal from different matrices to be explored as a technique for probing the interactions of the analyte metal with the matrix. A portion of the total Zn burden of fresh bovine liver slurry was rapidly mobilized in the absence of complexing agent, and the remainder was solubilized more rapidly than the Zn in a freeze-dried standard reference material of this tissue.

Animals↗

PubMed1991

Experimental apparatus for selection of adherent microorganisms under stringent growth conditions.

A bioreactor apparatus is described for studying bacterial attachment. A cyclic, on-off, flow regime was imposed within the apparatus. Model calculations illustrate the utility of this flow pattern in the selection and maintenance of slow-growing, adherent organisms. The apparatus is believed to have general utility in testing bacterial attachment influenced by many types of experimental or environmental constraints, including variations in fluid dynamics, presence of toxic substances (metals or organics), nature of the substratum surface, concentrations of limiting nutrients, and competition between bacterial strains. As an example application, the apparatus was employed to test 14 bacterial strains for surface attachment in a nutrient-limited growth medium. The medium was developed, using the chemical equilibrium program MINEQL, for planned studies of biofilms in a solution with a chemically defined composition that permits calculation of trace metal speciation. The apparatus was used to select organisms with growth and attachment characteristics that could not be evaluated by conventional batch, or chemostat, culture conditions. When supplied with acetate, pyruvate, or succinate as a carbon and energy source, the gram-negative strains Pseudomonas cepacia 17616 and Zoogloea sp. WGO4 showed superior attachment characteristics to glass surfaces in the chemically defined medium but only moderate fluid-phase growth. The gram-positive Arthrobacter sp. strain 9G4D and gram-negative species P. pickettii and Zoogloea sp. WNJ8, when supplied with pyruvate as a carbon and energy source, were capable of superior growth in the fluid phase but formed only a low to moderate biofilm surface coverage.

Bacteria↗

PubMed2001

The other chromatin.

Current understanding of heterochromatin, thanks to molecular data, focuses on its performing several functions in evolution and development. Heterochromatin shows characteristic distribution patterns in karyotypes and contributes to the broad scattering of genome sizes through biological taxa. Heterochromatin remains compacted and thus different from properly stained euchromatin during somatic interphase. A minimum amount of heterochromatin, however, is required for it to be visible in light microscopy. It may further escape notice during the dynamic processes of embryogenesis and gametogenesis. Present-day biology is in search of specific proteins and DNA sequences that comprise heterochromatin. The data that result from overcoming the threshold of visibility will support understanding of interference by heterochromatin in ontogeny and evolution. The contributions of Sigrid and Wolfgang Beermann to the study of heterochromation diminution (DNA elimination) are recalled, and we also discuss the functions and effects of heterochromatin on differential DNA endoreplication and in speciation.

Animals↗

PubMed2002

Revealing the faunal tapestry: co-evolution and historical biogeography of hosts and parasites in marine systems.

Parasites are integral components of marine ecosystems, a general observation accepted by parasitologists, but often considered of trifling significance to the broader community of zoologists. Parasites, however, represent elegant tools to explore the origins, distribution and maintenance of biodiversity. Among these diverse assemblages, host and geographic ranges described by various helminths are structured and historically constrained by genealogical and ecological associations that can be revealed and evaluated using phylogenetic methodologies within the context of frameworks and hypotheses for co-evolution and historical biogeography. Despite over 200 years of sporadic investigations of helminth systematics, knowledge of parasite faunal diversity in chondrichthyan and osteichthyan fishes, seabirds and marine mammals remains to be distilled into a coherent and comprehensive picture that can be assessed using phylogenetic approaches. Phylogenetic studies among complex host-parasite assemblages that encompass varying temporal and geographic scales are the critical context for elucidating biodiversity and faunal structure, and for identifying historical and contemporary determinants of ecological organization and biogeographic patterns across the marine biosphere. Insights from phylogenetic inference indicate (1) the great age of marine parasite faunas; (2) a significant role for colonization in diversification across a taxonomic continuum at deep and relatively recent temporal scales; and (3) a primary role for allopatric speciation. Integration of ecological and phylogenetic knowledge from the study of parasites is synergistic, contributing substantial insights into the history and maintenance of marine systems.

Animals↗

PubMed2001

The effect of habitat type on speciation rates and range movements in aquatic beetles: inferences from species-level phylogenies.

Most aquatic beetles in the family Dytiscidae are tightly associated either with running (lotic) or stagnant (lentic) water bodies. The range size of lotic species is known to be, on average, much smaller than that of lentic species, presumably as a result of differences in dispersal strategies in each habitat type. We explored possible effects of these differences on clade evolution and speciation rates by comparing species-level phylogenies based on cytochrome oxidase I (COI) and 16S rRNA mitochondrial genes for two genera, the lentic Ilybius and the lotic Deronectes. The expectation that species turnover is higher in lotic lineages due to their lower dispersal propensity compared to lentic species was not strongly supported. Deronectes displays a higher frequency of recent splits than Ilybius, consistent with the hypothesis, but the difference was not significant compared to expected patterns under a constant speciation rate null model. Similarly, when the degree of sympatry was plotted against relative node age, more allopatric splits were evident in the lentic Deronectes, suggesting a slower rate of range movement since speciation, but the differences were not significant. We discuss two explanations for our failure to detect differences between the two clades. First, current methods for analysing species-level phylogenies may be sensitive to taxonomic and sampling artefacts. Second, lentic and lotic clades may indeed display similar levels of species turnover despite occupying very different habitats at different spatial scales. More work is needed to investigate the effects of population level processes and spatial scale on macroevolutionary dynamics.

Animals↗

PubMed1967

The systematics of the Culex pipiens complex.

It was concluded in 1951 that the Culex pipiens complex could best be treated as a single polytypic species. Since then observations on morphologically and biologically intermediate forms have strengthened this conclusion. These observations are supported by the results of experimental work on temperature tolerances, winter diapause and mating behaviour and by crossing experiments. Discussions of the possible role of cytoplasmic isolating factors in initiating speciation within the complex have not been sufficiently conclusive. The relative fitness of hybrids may be more important in determining their rarity or otherwise in particular populations than the rather tenuous mating barriers so far demonstrated. Since 1951 two further forms-C. p. australicus and C. globocoxitus-have been added to the complex, and there is evidence of extensive replacement of C. p. pipiens by C. torrentium in England. It is therefore unwise to neglect the dynamic aspects or the geography of the complex. A comprehensive review of the morphological aspects of the complex is badly needed.

Animals↗

PubMed1998

"Reagentless" flow injection determination of ammonia and urea using membrane separation and solid phase basification.

Flow injection analysis instrumentation and methodology for the determination of ammonia and ammonium ions in an aqueous solution are described. Using in-line solid phase basification beds containing crystalline media. the speciation of ammoniacal nitrogen is shifted toward the un-ionized form. which diffuses in the gas phase across a hydrophobic microporous hollow fiber membrane into a pure-water-containing analytical stream. The two streams flow in a countercurrent configuration on opposite sides of the membrane. The neutral pH of the analytical stream promotes the formation of ammonium cations, which are detected using specific conductance. The methodology provides a lower limit of detection of 10 microgram/L and a dynamic concentration range spanning three orders of magnitude using a 315-microliters sample injection volume. Using immobilized urease to enzymatically promote the hydrolysis of urea to produce ammonia and carbon dioxide, the technique has been extended to the determination of urea.

Ammonia↗

PubMed2006

[Inductively coupled plasma mass spectrometry. Perspectives in analysis and in biology].

ICP-MS is an instrumental method of multi-elementary qualitative and quantitative analysis. It associates with a mass spectrometer (MS) an ion source composed of a plasma torch fed with inductive coupling with a high frequency electromagnetic generator (ICP), similar to that used as a light source in highly-successful Atomics Emission Spectrometry (AES). ICP-MS can be applied to simultaneous analysis of numerous metallic and metalloid elements (80 or so). Its sensitiveness is all in all far better than that available with previous spectrometric techniques, which nevertheless remain more advantageous for processing certain low atomic mass elements. Thanks to its broad dynamic range, ICP-MS allows quantification of an array of elementary concentrations within a single sample. ICP-MS offers particularly interesting perspectives in geochemistry and metal processing, as well as in biochemistry and food or toxicology and environmental analysis. Implementation is rapid and the technique is suitable for series or continuous analyses, or for analysis of any evolving medium such as effluents from gas or liquid chromatography or from capillary electrophoresis, making it a valuable tool for speciation analyses. Finally it enables non-radioactive isotopic labeling, essential for nutritional studies of trace elements, and sufficiently accurate isotopic dilutions, even with more accessible machines.

Animals↗

PubMed2003

Performance evaluation of two chelating ion-exchange sorbents for the fractionation of labile and inert metal species from aquatic media.

The performance of two iminodiacetate chelating resins, applied in an element fractionation scheme, was investigated for the characterization of marine and stream water samples collected in potentially contaminated harbor and industrial zones. The comparison involved an evaluation of the sorption/desorption behavior of Cd, Cu, Pb and Zn on Chelex-100, a sorbent extensively employed for metal speciation studies, and on Lewatit TP-207, a material with similar chelating characteristics for which no applications for fractionation studies are reported. A characterization of the latter resin in terms of the influence of sample pH on the uptake of metals from aqueous solutions and their subsequent acid elution was carried out. Fractionation studies were performed on natural water samples and model solutions resembling their composition, spiked with micromolar concentrations of the metals. The operationally defined fractionation scheme is based on dynamic adsorption of the resin-labile fractions of metals on microcolumns made of the sorbents. This stage is followed by a batch procedure in which the eluent from the column is contacted with fresh resin to discriminate between the relatively stable species unable to react with the resin during the column interaction time, and the strongly complexed metals that do not interact with the sorbent even for periods of several hours. Results were obtained from coarsely filtered sub-samples and from specimens passed through membrane filters of pore size 0.45 and 0.22 microm. The method was also assessed with model solutions of the metals containing variable concentrations (in the 10(-3)-10(-7) molar range) of complex forming agents such as nitrilotriacetic acid and trans-1,2-diaminocyclohexane-N,N,N',N'-tetraacetic acid. An additional batch method, in which a fixed amount of resin was contacted with sample solution for increasing periods of time and the amount of metal remaining in solution measured as a function of the elapsed time, was used to obtain information on the kinetics of dissociation of species formed in the presence of added complexants. The behavior of both resins was similar, demonstrating that the discrimination of species derived from experiments with Chelex-100 may be properly validated by independent fractionation tests carried out with Lewatit TP-207. The behavior of the sorbents is also discussed in terms of the possible influence of particulate or colloidal materials and of kinetic effects related to the presence of complexing agents.

Journal Article↗

PubMed2003

Reproductive character displacement and the genetics of gamete recognition in tropical sea urchins.

Reproductive character displacement occurs when sympatric and allopatric populations of a species differ in traits crucial to reproduction, and it is commonly thought of as a signal of selection acting to limit hybridization. Most documented cases of reproductive character displacement involve characters that are poorly understood at the genetic level, and rejecting alternative hypotheses for biogeographic shifts in reproductive traits is often very difficult. In sea urchins, the gamete recognition protein bindin evolves under positive selection when species are broadly sympatric, suggesting character displacement may be operating in this system. We sampled sympatric and allopatric populations of two species in the sea urchin genus Echinometra for variation in bindin and for the mitochondrial cytochrome oxidase I to examine patterns of population differentiation and molecular evolution at a reproductive gene. We found a major shift in bindin alleles between central Pacific (allopatric) and western Pacific (sympatric) populations of E. oblonga. Allopatric populations of E. oblonga are polyphyletic with E. sp. C at bindin, whereas sympatric populations of the two species are reciprocally monophyletic. There is a strong signal of positive selection (P(N)/P(S) = 4.5) in the variable region of the first exon of bindin, which is associated with alleles found in sympatric populations of E. oblonga. These results indicate that there is a strong pattern of reproductive character displacement between E. oblonga and E. sp. C and that the divergence is driven by selection. There is much higher population structure in sympatric populations at the bindin locus than at the neutral mitochondrial locus, but this difference is not seen in allopatric populations. These data suggest a pattern of speciation driven by selection for local gamete coevolution as a result of interactions between sympatric species. Although this pattern is highly suggestive of speciation by reinforcement, further research into hybrid fitness and egg-sperm interactions is required to address this potential mechanism for character displacement.

Amino Acid Sequence↗

PubMed2005

Comparative landscape genetics and the adaptive radiation of Darwin's finches: the role of peripheral isolation.

We use genetic divergence at 16 microsatellite loci to investigate how geographical features of the Galápagos landscape structure island populations of Darwin's finches. We compare the three most genetically divergent groups of Darwin's finches comprising morphologically and ecologically similar allopatric populations: the cactus finches (Geospiza scandens and Geospiza conirostris), the sharp-beaked ground finches (Geospiza difficilis) and the warbler finches (Certhidea olivacea and Certhidea fusca). Evidence of reduced genetic diversity due to drift was limited to warbler finches on small, peripheral islands. Evidence of low levels of recent interisland migration was widespread throughout all three groups. The hypothesis of distance-limited dispersal received the strongest support in cactus and sharp-beaked ground finches as evidenced by patterns of isolation by distance, while warbler finches showed a weaker relationship. Support for the hypothesis that gene flow constrains morphological divergence was only found in one of eight comparisons within these groups. Among warbler finches, genetic divergence was relatively high while phenotypic divergence was low, implicating stabilizing selection rather than constraint due to gene flow. We conclude that the adaptive radiation of Darwin's finches has occurred in the presence of ongoing but low levels of gene flow caused by distance-dependent interisland dispersal. Gene flow does not constrain phenotypic divergence, but may augment genetic variation and facilitate evolution due to natural selection. Both microsatellites and mtDNA agree in that subsets of peripheral populations of two older groups are genetically more similar to other species that underwent dramatic morphological change. The apparent decoupling of morphological and molecular evolution may be accounted for by a modification of Lack's two-stage model of speciation: relative ecological stasis in allopatry followed by secondary contact, ecological interactions and asymmetric phenotypic divergence.

Adaptation, Biological↗

PubMed1998

Slow rate of molecular evolution in high-elevation hummingbirds.

Estimates of relative rates of molecular evolution from a DNA-hybridization phylogeny for 26 hummingbird species provide evidence for a negative association between elevation and rate of single-copy genome evolution. This effect of elevation on rate remains significant even after taking into account a significant negative association between body mass and molecular rate. Population-level processes do not appear to account for these patterns because (i) all hummingbirds breed within their first year and (ii) the more extensive subdivision and speciation of bird populations living at high elevations predicts a positive association between elevation and rate. The negative association between body mass and molecular rate in other organisms has been attributed to higher mutation rates in forms with higher oxidative metabolism. As ambient oxygen tensions and temperature decrease with elevation, the slow rate of molecular evolution in high-elevation hummingbirds also may have a metabolic basis. A slower rate of single-copy DNA change at higher elevations suggests that the dynamics of molecular evolution cannot be separated from the environmental context.

Animals↗

PubMed2003

No evidence for parallel sympatric speciation in cichlid species of the genus Pseudotropheus from north-western Lake Malawi.

To test the hypothesis of parallel speciation by sexual selection, we examined length variation at six microsatellite loci of samples from four sites of four to six putative species belonging to two subgenera of rocky shore mbuna cichlids from Lake Malawi. Almost all fixation indices were significantly different from zero, suggesting that there is presently little or no gene flow among allopatric populations or sympatric species. Analysis of variance indicated that genetic distances among allopatric populations of putative conspecifics were significantly lower than among sympatric populations of heterospecifics. The topology of trees based on distance matrices was also largely consistent with the hypothesis that the putative species are monophyletic and have thus not evolved in parallel in their present locations. If parallel speciation does occur in Malawi cichlids, it may be on a larger spatial scale than investigated in our study.

Alleles↗

PubMed2005

Genetic structure in Orchesella cincta (Collembola): strong subdivision of European populations inferred from mtDNA and AFLP markers.

Population genetic structure is determined both by current processes and historical events. Current processes include gene flow, which is largely influenced by the migration capacity of a species. Historical events are, for example, glaciation periods, which have had a major impact on the distribution of many species. Species with a low capacity or tendency to move about or disperse often exhibit clear spatial genetic structures, whereas mobile species mostly show less spatial genetic differentiation. In this paper we report on the genetic structure of a small, wingless arthropod species (Orchesella cincta: Collembola) in Europe. For this purpose we used mtDNA COII sequences and AFLP markers. We show that large genetic differences exist between populations of O. cincta, as expected from O. cincta's winglessness and sedentary lifestyle. Despite the fact that most variability was observed within populations (59%), a highly significant amount of AFLP variation (25%) was observed between populations from northwestern Europe, central Europe and Italy. This suggests that gene flow among regions is extremely low, which is additionally supported by the lack of shared mtDNA alleles between regions. Based on the genetic variation and sequence differences observed we conclude that the subdivision occurred long before the last glaciation periods. Although the populations still interbreed in the lab, we assume that in the long term the genetic isolation of these regions may lead to speciation processes.

Analysis of Variance↗

PubMed2003

Analytical solution of a neutral model of biodiversity.

The unified neutral model of biodiversity proposed by S. Hubbell is solved analytically: The distributions of species abundance in the metacommunity and in a local community are calculated exactly as a function of speciation and migration rates and of the size of the community. In the limit of large population sizes the densities of species of given relative abundance are found to be given by universal functions depending only on two parameters.

Biodiversity↗

PubMed2002

Effect of initial cell density on the bioavailability and toxicity of copper in microalgal bioassays.

Algal toxicity tests based on growth inhibition over 72 h have been extensively used to assess the toxicity of contaminants in natural waters. However, these laboratory tests use high cell densities compared to those found in aquatic systems in order to obtain a measurable algal response. The high cell densities and test duration can result in changes in chemical speciation, bioavailability, and toxicity of contaminants throughout the test. With the recent application of flow cytometry to ecotoxicology, it is now possible to use lower initial cell densities to minimize chemical speciation changes. The speciation and toxicity of copper in static bioassays with the tropical freshwater alga Chlorella sp. and the temperate species Selenastrum capricornutum (Pseudokirchneriella subcapitata) were investigated at a range of initial cell densities (10(2)-10(5) cells/ml). Copper toxicity decreased with increasing initial cell density. Copper concentrations required to inhibit growth (cell division) rate by 50% (72-h median effective concentration [EC50]) increased from 4.6 to 16 microg/L for Chlorella sp. and from 6.6 to 17 microg/L for S. capricornutum as the initial cell density increased from 10(2) to 10(5) cells/ml. Measurements of anodic stripping voltammetry-labile, extracellular, and intracellular copper confirmed that at higher initial cell densities, less copper was bound to the cells, resulting in less copper uptake and lower toxicity. Chemical measurements indicated that reduced copper toxicity was due primarily to depletion of dissolved copper in solution, with solution speciation changes due to algal exudates and pH playing a minor role. These findings suggest that standard static laboratory bioassays using 10(4) to 10(5) algal cells/ml may seriously underestimate metal toxicity in natural waters.

Biological Availability↗

PubMed2000

Adaptive dynamics in diploid, sexual populations and the evolution of reproductive isolation.

Evolutionary branching is the process whereby an initially monomorphic population evolves to a point where it undergoes disruptive selection and splits up into two phenotypically diverging lineages. We studied evolutionary branching in three models that are ecologically identical but that have different genetic systems. The first model is clonal, the second is sexual diploid with additive genetics on a single locus and the third is like the second but with an additional locus for mate choice. Evolutionary branching occurred under exactly the same ecological circumstances in all three models. After branching the evolutionary dynamics may be qualitatively different. In particular, in the diploid, sexual models there can be multiple evolutionary outcomes whereas in the corresponding clonal model there is only one. We showed that evolutionary branching favours the evolution of (partial) assortative mating and that this in turn effectively restores the results from the clonal model by rendering the alternative outcomes unreachable except for the one that also occurs in the clonal model. The evolution of assortative mating during evolutionary branching can be interpreted as the initial phase of sympatric speciation with phenotypic divergence and partial reproductive isolation.

Adaptation, Physiological↗