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PubMed2000

Estimation of primate speciation dates using local molecular clocks.

Protein-coding genes of the mitochondrial genomes from 31 mammalian species were analyzed to estimate the speciation dates within primates and also between rats and mice. Three calibration points were used based on paleontological data: one at 20-25 MYA for the hominoid/cercopithecoid divergence, one at 53-57 MYA for the cetacean/artiodactyl divergence, and the third at 110-130 MYA for the metatherian/eutherian divergence. Both the nucleotide and the amino acid sequences were analyzed, producing conflicting results. The global molecular clock was clearly violated for both the nucleotide and the amino acid data. Models of local clocks were implemented using maximum likelihood, allowing different evolutionary rates for some lineages while assuming rate constancy in others. Surprisingly, the highly divergent third codon positions appeared to contain phylogenetic information and produced more sensible estimates of primate divergence dates than did the amino acid sequences. Estimated dates varied considerably depending on the data type, the calibration point, and the substitution model but differed little among the four tree topologies used. We conclude that the calibration derived from the primate fossil record is too recent to be reliable; we also point out a number of problems in date estimation when the molecular clock does not hold. Despite these obstacles, we derived estimates of primate divergence dates that were well supported by the data and were generally consistent with the paleontological record. Estimation of the mouse-rat divergence date, however, was problematic.

Animals↗
PubMed2001

Ancient diversification of the Pto kinase family preceded speciation in Solanum.

Recent phylogenetic analyses of the nucleotide binding sites (NBS)-leucine-rich repeats (LRR) class of plant disease resistance (R) genes suggest that these genes are ancient and coexist next to susceptibility alleles at resistance loci. Another class of R genes encodes serine-threonine protein kinases related to Pto that were originally identified from wild relatives of tomato. In this study, we exploit the highly diverse genus Solanum to identify Pto-like sequences and test various evolutionary scenarios for Pto-like genes. Polymerase chain reaction amplifications with the use of primers that were developed on the basis of conserved and variable regions of Pto revealed an extensive Pto gene family and yielded 32 intact Pto-like sequences from six Solanum species. Furthermore, Pto-like transcripts were detected in the leaf tissue of all tested plants. The kinase consensus and autophosphorylation sites were highly conserved, in contrast to the kinase activation domain, which is involved in ligand recognition in Pto. Phylogenetic analyses distinguished nine classes of Pto-like genes and revealed that orthologs were more similar than paralogs, suggesting that the Pto gene family evolved through a series of ancient gene duplication events prior to speciation in Solanum. Thus, like the NBS-LRR class, the kinase class of R genes is highly diverse and ancient.

Amino Acid Sequence↗
PubMed2000

A radioiodine speciation, deposition, and dispersion model with uncertainty propagation for the Oak Ridge dose reconstruction.

Between 1944 and 1956, radioactive 131I was released into the atmosphere from operations at the Oak Ridge National Laboratory in Oak Ridge, TN. The releases occurred from stacks and from building vents and openings in three different chemical forms: elemental, organic, and particulate. During their transport in the atmosphere, different forms of iodine react differently with other atmospheric chemicals and moisture, and are removed from the plume at different rates by the processes of dry and wet deposition. A modified Gaussian plume model was developed to address the processes of radioiodine speciation, deposition, depletion, and dispersion in the atmosphere, and to propagate uncertainties in input parameter values through to the ground-level concentrations of 131I in air. A unique approach was used to develop an implicitly correlated set of hourly meteorological parameters for any day of a month for each month of the year from ten years of available data between 1987 and 1996. The model was validated for both annual average and short-term releases. For the annual average releases, the predictions of ground-level concentrations of 131I from the model were within a factor of 2 of measured field data. For two of the three sets of available weekly data, the measurements fell within the 95% subjective confidence interval of model predictions. Predictions of ground-level air concentrations were made on an annual average basis for the entire period of release and on a short-term, episodic basis for a 1954 accident.

Atmosphere↗
PubMed2000

The impact of plutonium speciation on the distribution coefficients in a sediment-sea water system, and radiological assessment of doses to humans.

When radionuclides are released from a source into the marine environment, the assessment of long term consequences to humans depends on information on the source term, transport in water, interactions with sediments (KD) and biological uptake (CF). Sensitivity analysis of assessment models demonstrates that KD is one of the most sensitive parameters contributing to large uncertainties in the assessment. Furthermore, the interaction of Pu-species with sediments is a time and temperature dependent process. The distribution coefficient, Bq kg(-1) sediment per Bq L(-1) sea water, increases with time until pseudo-equilibrium/equilibrium is reached (KD). Thus, the contact time between contaminated sea water and sediments should be taken into account in dispersion and dose assessment models. In the present work, dynamic tracer experiments have been performed where different Pu-species are added to a sediment-sea water system to obtain information on KD's. After a defined contact time, the samples have been sequentially extracted to determine mobile and bound fractions. The results indicate that the distribution coefficient, KD, for plutonium depends on Pu-species in question. Thus, sediments act as a sink for Pu(III, IV) (high KD), while Pu(III, IV)-organic and Pu(V, VI) should be considered more mobile (low KD). Furthermore, the interaction with inert fractions obtained from sequential extraction depends less on Pu-species but increase with time. For short time interactions, species-specific time functions rather than KD constants should be applied in assessment models. When the accepted KD (10(5) L kg(-1)) is implemented in the model, the estimated collective dose is about 8 x 10(-4) person-Sv, i.e., a factor of about 2 lower than for Pu(III, IV)-organic and Pu(V, VI). So changes in KD have an impact on the assessment of collective dose received from a potential release of plutonium from fallout, reactor accidents, etc., which underlines the need for more detailed studies on speciation, kinetics, and KD's in different sediment-sea water systems.

Acetates↗
PubMed2003

Radionuclide speciation in effluent from La Hague reprocessing plant in France.

Effluent from the La Hague nuclear fuel reprocessing plant was mixed with seawater in order to investigate the fate of the various radionuclides. Thus, a major objective of the present work is to characterize the effluent from La Hague reprocessing plant and to study how the radionuclide speciation changes with time when discharged into the marine environment. Discharges from the La Hague nuclear reprocessing plant represent an important source of artificially produced radionuclides to the North Sea. The transport, distribution, and biological uptake of radionuclides in the marine environment depends, however, on the physicochemical forms of radionuclides in the discharged effluents and on transformation processes that occur after entering the coastal waters. Information of these processes is needed to understand the transport and long-term distribution of the radionuclides. In the present work, a weekly discharged effluent from the nuclear fuel reprocessing plant at Cap La Hague in France was mixed with coastal water and fractionated with respect to particle size and charged species using ultra centrifugation and hollow fiber ultrafiltration with on line ion exchange. The size distribution pattern of gamma-emitting radionuclides was followed during a 62-h period after mixing the effluent with seawater. 54Mn was present as particulate material in the effluent, while other investigated radionuclides were discharged in a more mobile form or were mobilized after mixing with sea water (e.g., 60Co) and can be transported long distances in the sea. Sediments can act as a sink for less mobile discharged radionuclides (Skipperud et al. 2000). A kinetic model experiment was performed to provide information of the time-dependent distribution coefficients, Kd (t). The retention of the effluent radionuclides in sediments was surprisingly low (Kd 20-50), and the sediments acted as a poor sink for the released radionuclides. Due to the presence of non-reacting radionuclide species in the effluent, a major fraction of the radionuclides, such as Cs-isotopes, 106Ru and 125Sb, in the effluent will be subjected to marine transport to the Northern Seas (i.e., the North Sea, Norwegian Sea and the Barents Sea). The La Hague effluent may, therefore, contribute to enriched levels of radionuclides found in the English Channel, including 90Sr, 60Co and Pu-isotopes, and also 106Ru and 125Sb.

France↗
PubMed1997

In situ hybridization for Aspergillus and Penicillium in allergic fungal sinusitis: a rapid means of speciating fungal pathogens in tissues.

Allergic fungal sinusitis (AFS) is a serious form of sinonasal fungal disease that is commonly associated with Aspergillus or Dematiaceous fungi. This study was performed to determine the incidence of Aspergillus or Penicillium in AFS by using in situ hybridization (ISH) for Aspergillus and Penicillium ribosomal RNA (rRNA). The Fontana-Masson melanin stain (FMMS) was also used to detect pigmented fungi (A. niger and Dematiaceous fungi). ISH was performed on 26 patients: 17 AFS cases with histologic evidence of fungi, 5 AFS cases without histologic evidence of fungi, 3 cases of invasive fungal sinusitis (IFS), and 1 case of fungus ball. Nine AFS specimens with histologic evidence of fungi were ISH positive. Positivity was also noted in two of three IFS cases, while no staining was seen in the fungus ball and in six AFS specimens without fungi demonstrable by silver stains. Six ISH-positive cases were FMMS positive, suggesting A. niger. Five ISH-negative AFS specimens were FMMS positive, suggesting Dematiaceous fungi. In summary, many AFS patients in our institution demonstrate Aspergillus/Penicillium organisms. Ancillary techniques may help identify fungi responsible for AFS if cultures are negative or not performed. ISH for rRNA is a useful means for rapidly speciating fungi in human tissues.

Adult↗
PubMedDate not supplied

Evaluation of modified New York City carbohydrate medium for the speciation of Neisseria.

A comparative study of modified New York City carbohydrate medium, Minitek (BBL Microbiology Systems, Cockeysville, Md.) and cystine-trypticase agar was conducted for determination of the relative accuracies of these media in the identification of pathogenic Neisseria. Of 170 isolates of Neisseria gonorrhoeae, 169 were correctly identified by New York City carbohydrate media, 131 by Minitek, and 117 by cystine-trypticase agar. Of the 72 isolates of Neisseria meningitidis tested, all were accurately speciated by New York City carbohydrate media, whereas Minitek and cystine-trypticase agar identified 61 and 49 strains, respectively. The greater reliability of New York City carbohydrate media is accompanied by advantages not offered by the other media.

Agar↗
PubMed1997

Genetic distinctiveness of a village population of house mice: relevance to speciation and chromosomal evolution.

A population of house mice, Mus musculus domesticus, from the village of Migiondo was found to be genetically distinct from nearby populations in Upper Valtellina (Italian Alps). At the supernatant malic enzyme locus, Mod1, the only alleles found in Migiondo (c and n2) were virtually absent from the other populations in the valley, which were characterized by allele a. The extraordinary genetic distinctiveness of the Migiondo population is apparently the result of genetic drift, perhaps coupled with a founder event, and attests to the existence of nearly impenetrable geographic barriers around the village isolating it from other settlements only a few hundred metres away. The Mod1 features of the house mice in Migiondo are reminiscent of the characteristics of house mice on maritime islands. The genetic confirmation of the geographic isolation of Migiondo is of interest because there is evidence that this village may have been the site of recent speciation and extinction events. The data are also of significance given the phenomenal chromosomal variation in house mice from the vicinity of the Alps. It has frequently been proposed that genetic drift/founder events are of importance in the fixation of chromosomal rearrangements; this study provides the first direct evidence for their occurrence in alpine mouse populations.

Alleles↗
PubMed2000

Historical contingency and ecological determinism interact to prime speciation in sticklebacks, Gasterosteus.

Historical contingency and determinism are often cast as opposing paradigms under which evolutionary diversification operates. It may be, however, that both factors act together to promote evolutionary divergence, although there are few examples of such interaction in nature. We tested phylogenetic predictions of an explicit historical model of divergence (double invasions of freshwater by marine ancestors) in sympatric species of three-spined sticklebacks (Gasterosteus aculeatus) where determinism has been implicated as an important factor driving evolutionary novelty. Microsatellite DNA variation at six loci revealed relatively low genetic variation in freshwater populations, supporting the hypothesis that they were derived by colonization of freshwater by more diverse marine ancestors. Phylogenetic and genetic distance analyses suggested that pairs of sympatric species have evolved multiple times, further implicating determinism as a factor in speciation. Our data also supported predictions based on the hypothesis that the evolution of sympatric species was contingent upon 'double invasions' of postglacial lakes by ancestral marine sticklebacks. Sympatric sticklebacks, therefore, provide an example of adaptive radiation by determinism contingent upon historical conditions promoting unique ecological interactions, and illustrate how contingency and determinism may interact to generate geographical variation in species diversity

Alleles↗
PubMed2001

Disruptive sexual selection against hybrids contributes to speciation between Heliconius cydno and Heliconius melpomene.

Understanding the fate of hybrids in wild populations is fundamental to understanding speciation. Here we provide evidence for disruptive sexual selection against hybrids between Heliconius cydno and Heliconius melpomene. The two species are sympatric across most of Central and Andean South America, and coexist despite a low level of hybridization. No-choice mating experiments show strong assortative mating between the species. Hybrids mate readily with one another, but both sexes show a reduction in mating success of over 50% with the parental species. Mating preference is associated with a shift in the adult colour pattern, which is involved in predator defence through Müllerian mimicry, but also strongly affects male courtship probability. The hybrids, which lie outside the curve of protection afforded by mimetic resemblance to the parental species, are also largely outside the curves of parental mating preference. Disruptive sexual selection against F(1) hybrids therefore forms an additional post-mating barrier to gene flow, blurring the distinction between pre-mating and post-mating isolation, and helping to maintain the distinctness of these hybridizing species.

Animals↗
PubMed2003

Sex chromosome evolution and speciation in Ficedula flycatchers.

Speciation is the combination of evolutionary processes that leads to the reproductive isolation of different populations. We investigate the significance of sex-chromosome evolution on the development of post- and prezygotic isolation in two naturally hybridizing Ficedula flycatcher species. Applying a tag-array-based mini-sequencing assay to genotype single nucleotide polymorphisms (SNPs) and interspecific substitutions, we demonstrate rather extensive hybridization and backcrossing in sympatry. However, gene flow across the partial postzygotic barrier (introgression) is almost exclusively restricted to autosomal loci, suggesting strong selection against introgression of sex-linked genes. In addition to this partial postzygotic barrier, character displacement of male plumage characteristics has previously been shown to reinforce prezygotic isolation in these birds. We show that male plumage traits involved in reinforcing prezygotic isolation are sex linked. These results suggest a major role of sex-chromosome evolution in mediating post- and prezygotic barriers to gene flow and point to a causal link in the development of the two forms of reproductive isolation.

Animals↗
PubMed2004

Ice sheets promote speciation in boreal birds.

The premise that Pleistocene ice ages played an important role in generating present-day species diversity has been challenged by genetic data indicating that most of the youngest terrestrial species on Earth coalesced long before major glacial advances. However, study has been biased towards faunas distributed at low latitudes that were not directly fragmented by advancing ice sheets. Using mitochondrial sequence divergence and a molecular clock, we compared the coalescence times of pairs of avian species belonging to superspecies complexes from the high-latitude boreal forest with those of sub-boreal and tropical avifaunas of the New World. Remarkably, all coalescence events in boreal superspecies date to the Pleistocene, providing direct evidence that speciation was commonly initiated during recent glacial periods. A pattern of endemism in boreal superspecies plausibly links the timing of divergence to the fragmentation of the boreal forest by ice sheets during the Mid- and Late Pleistocene. In contrast to the boreal superspecies, only 56% of sub-boreal and 46% of tropical superspecies members coalesced during the Pleistocene, suggesting that avifaunas directly fragmented by ice sheets experienced rapid rates of diversification, whereas those distributed farther south were affected to a lesser extent. One explanation for the absence of pre-Pleistocene superspecies in boreal avifaunas is that strong selection pressures operated in boreal refugia, causing superspecies members to achieve ecological differentiation at an accelerated rate.

Animals↗
PubMed2004

Intraspecific sexual selection on a speciation trait, male coloration, in the Lake Victoria cichlid Pundamilia nyererei.

The haplochromine cichlids of Lake Victoria constitute a classical example of explosive speciation. Extensive intra- and interspecific variation in male nuptial coloration and female mating preferences, in the absence of postzygotic isolation between species, has inspired the hypothesis that sexual selection has been a driving force in the origin of this species flock. This hypothesis rests on the premise that the phenotypic traits that underlie behavioural reproductive isolation between sister species diverged under sexual selection within a species. We test this premise in a Lake Victoria cichlid, by using laboratory experiments and field observations. We report that a male colour trait, which has previously been shown to be important for behavioural reproductive isolation between this species and a close relative, is under directional sexual selection by female mate choice within this species. This is consistent with the hypothesis that female choice has driven the divergence in male coloration between the two species. We also find that male territoriality is vital for male reproductive success and that multiple mating by females is common.

Animals↗
PubMed2004

Historical climate change and speciation: neotropical seasonally dry forest plants show patterns of both tertiary and quaternary diversification.

Historical climate changes have had a major effect on the distribution and evolution of plant species in the neotropics. What is more controversial is whether relatively recent Pleistocene climatic changes have driven speciation, or whether neotropical species diversity is more ancient. This question is addressed using evolutionary rate analysis of sequence data of nuclear ribosomal internal transcribed spacers in diverse taxa occupying neotropical seasonally dry forests, including Ruprechtia (Polygonaceae), robinioid legumes (Fabaceae), Chaetocalyx and Nissolia (Fabaceae), and Loxopterygium (Anacardiaceae). Species diversifications in these taxa occurred both during and before the Pleistocene in Central America, but were primarily pre-Pleistocene in South America. This indicates plausibility both for models that predict tropical species diversity to be recent and that invoke a role for Pleistocene climatic change, and those that consider it ancient and implicate geological factors such as the Andean orogeny and the closure of the Panama Isthmus. Cladistic vicariance analysis was attempted to identify common factors underlying evolution in these groups. In spite of the similar Mid-Miocene to Pliocene ages of the study taxa, and their high degree of endemism in the different fragments of South American dry forests, the analysis yielded equivocal, non-robust patterns of area relationships.

Base Sequence↗
PubMed2006

Real-time PCR detection and speciation of Cryptosporidium infection using Scorpion probes.

At least eight species of Cryptosporidium can cause human infection and disease. A real-time PCR (qPCR) assay based on the 18S rRNA gene and utilizing a Scorpion probe was developed to detect all human-pathogenic Cryptosporidium without the usual need for nested amplification. Sensitivity of detection in stool samples was highest using a glass bead-based DNA extraction method (under 10(3) oocysts per stool sample). The assay was validated against 123 human stool specimens from Bangladesh and Tanzania, exhibited a sensitivity and specificity of >91% versus microscopy, and detected an additional eight microscopy-negative infections. Cryptosporidium parvum-specific and Cryptosporidium meleagridis-specific Scorpion qPCR assays that provided 100% accurate speciation compared with VspI RFLP analysis and sequencing were developed subsequently. These Scorpion probe qPCR assays are simpler to perform than existing nested PCR and RFLP methods for diagnosis and epidemiological investigation of cryptosporidiosis.

Animals↗
PubMed2002

Innovations in the speciation of organolead compounds in water: towards a more rational, rapid, and simple analytical process.

Speciation analysis calls for rapid, simple systems for minimizing errors made in the most troublesome of all steps in the analytical process: sample preparation. In this context, continuous-flow systems are of great help. The evolution in the different methodologies enabled solutions to the main shortcomings occurring from the lack of selectivity of using RP-C18 as sorbent material. One solution was a shift to more sensitive and selective, but only partially automated, systems employing C60 fullerene and Grignard's reagent; another was a shift to completely automated systems employing sodium tetrapropylborate; and a final solution was to employ the simplest possible configuration by removing the reagent stream. The analytical methods developed allowed the identification and quantification of different organolead species at the pg/ml levels in rainwater samples, with precision (RSD) of about 5% and recoveries ranging from 92 to 100%.

Automation↗
PubMed2004

Human, mouse, and rat genome large-scale rearrangements: stability versus speciation.

Using paired-end sequences from bacterial artificial chromosomes, we have constructed high-resolution synteny and rearrangement breakpoint maps among human, mouse, and rat genomes. Among the >300 syntenic blocks identified are segments of over 40 Mb without any detected interspecies rearrangements, as well as regions with frequently broken synteny and extensive rearrangements. As closely related species, mouse and rat share the majority of the breakpoints and often have the same types of rearrangements when compared with the human genome. However, the breakpoints not shared between them indicate that mouse rearrangements are more often interchromosomal, whereas intrachromosomal rearrangements are more prominent in rat. Centromeres may have played a significant role in reorganizing a number of chromosomes in all three species. The comparison of the three species indicates that genome rearrangements follow a path that accommodates a delicate balance between maintaining a basic structure underlying all mammalian species and permitting variations that are necessary for speciation.

Animals↗
PubMed2001

Simulated ecology-driven sympatric speciation.

We introduce a multilocus genetically acquired phenotype, submitted to mutations and with selective value, in an age-structured model for biological aging. This phenotype describes a single-trait effect of the environment on an individual, and we study the resulting distribution of this trait among the population. In particular, our simulations show that the appearance of a double phenotypic attractor in the ecology induces the emergence of a stable polymorphism, as observed in the Galapagos finches. In the presence of this polymorphism, the simulations generate short-term speciation, when mating preferences are also allowed to suffer mutations and acquire selective value.

Animals↗