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Phosphorus speciation in manure-amended alkaline soils.

Two common manure storage practices are stockpiles and lagoons. The manure from stockpiles is applied to soils in solid form, while lagoon manure is applied as a liquid. Soil amendment with manure in any form introduces a significant amount of phosphorus (P) that exists in both organic and inorganic forms. However, little is known about P speciation in manure stored under different conditions, or the subsequent forms when applied to soils. We used solution (31)P nuclear magnetic resonance (NMR) spectroscopy and conventional P fractionation and speciation methods to investigate P forms in dairy manure and liquid lagoon manure, and to study how long-term amendment with these manures influenced surface and subsurface soil P speciation. Our results show that the P forms in solid and lagoon manure are similar. About 30% of the total P was organic, mostly as orthophosphate monoesters. On a dry weight basis, total P was much higher in the solid manure. In the manure-amended soils the total P concentrations of the surface soils were similar, regardless of manure type. Total P in the subsurface soil was greater in the lagoon-manure-amended soil than the solid-manure-amended subsurface soil. However, the fraction of organic P was greater in the subsurface of the solid-manure-amended soil. The NMR results indicate that the majority of organic P in the soils is phytic acid, which is enriched in the surface soils compared with the subsurface soils. These results provide insight into P speciation and dynamics in manure-amended soils that will further increase our understanding on how best to manage manure disposal on soils.

Animals↗
PubMed2005

Rapid cladogenesis in marine fishes revisited.

Lineages that underwent rapid cladogenesis are attractive systems for the study of mechanisms underlying taxonomic, ecological, morphological, and behavioral diversification. Recently developed statistical methods provide insights into historical patterns of diversity and allow distinguishing bursts of cladogenesis from stochastic background rates in the presence of confounding factors such as extinction and incomplete taxon sampling. Here, we compare the dynamics of speciation in several marine fish lineages some of which were previously proposed to have undergone significant changes of cladogenesis through time. We tested for evidence of episodes of rapid cladogenesis using the constant rate and Monte Carlo constant rate tests that are robust to incomplete taxon sampling. These tests employ the statistic gamma to measure the relative position of internal node in a chronogram. For the first time, we conducted a comparative analysis to address the behavior of the statistic under different chronogram-constructing methods (Langley-Fitch, nonparametric rate smoothing, and penalized likelihood). Although estimates of gamma sometimes differ widely among methods, acceptance or rejection of the constant rate model within a particular clade appears to be robust to the choice of method. Bursts of cladogenesis were detected in 14 of 34 studied datasets. Some of these were previously proposed to represent marine fish "radiations," whereas others are identified anew. Our results indicate that the wider application of tree shape methods that are able to detect significantly elevated rates of speciation is useful to more precisely define clades that underwent episodes of rapid cladogenesis in marine fish clades. Contrasting the patterns of phylogenetic diversification in marine fish lineages may facilitate the identification of common evolutionary trajectories versus idiosyncrasies, and ultimately help towards a better understanding of the factors and processes underlying speciation in the marine realm.

Animals↗
PubMed2004

Application of Johnson et al.'s speciation threshold model to apparent colonization times of island biotas.

Understanding patterns of diversity can be furthered by analysis of the dynamics of colonization, speciation, and extinction on islands using historical information provided by molecular phylogeography. The land birds of the Lesser Antilles are one of the most thoroughly described regional faunas in this context. In an analysis of colonization times, Ricklefs and Bermingham (2001) found that the cumulative distribution of lineages with respect to increasing time since colonization exhibits a striking change in slope at a genetic distance of about 2% mitochondrial DNA sequence divergence (about one million years). They further showed how this heterogeneity could be explained by either an abrupt increase in colonization rates or a mass extinction event. Cherry et al. (2002), referring to a model developed by Johnson et al. (2000), argued instead that the pattern resulted from a speciation threshold for reproductive isolation of island populations from their continental source populations. Prior to this threshold, genetic divergence is slowed by migration from the source, and species of varying age accumulate at a low genetic distance. After the threshold is reached, source and island populations diverge more rapidly, creating heterogeneity in the distribution of apparent ages of island taxa. We simulated of Johnson et al.'s speciation-threshold model, incorporating genetic divergence at rate k and fixation at rate M of genes that have migrated between the source and the island population. Fixation resets the divergence clock to zero. The speciation-threshold model fits the distribution of divergence times of Lesser Antillean birds well with biologically plausible parameter estimates. Application of the model to the Hawaiian avifauna, which does not exhibit marked heterogeneity of genetic divergence, and the West Indian herpetofauna, which does, required unreasonably high migration-fixation rates, several orders of magnitude greater than the colonization rate. However, the plausibility of the speciation-divergence model for Lesser Antillean birds emphasizes the importance of further investigation of historical biogeography on a regional scale for whole biotas, as well as the migration of genes between populations on long time scales and the achievement of reproductive isolation.

Animals↗
PubMed2000

Millennial-scale dynamics of southern Amazonian rain forests.

Amazonian rain forest-savanna boundaries are highly sensitive to climatic change and may also play an important role in rain forest speciation. However, their dynamics over millennial time scales are poorly understood. Here, we present late Quaternary pollen records from the southern margin of Amazonia, which show that the humid evergreen rain forests of eastern Bolivia have been expanding southward over the past 3000 years and that their present-day limit represents the southernmost extent of Amazonian rain forest over at least the past 50,000 years. This rain forest expansion is attributed to increased seasonal latitudinal migration of the Intertropical Convergence Zone, which can in turn be explained by Milankovitch astronomic forcing.

Bolivia↗
PubMed2000

Waiting time to parapatric speciation.

Using a weak migration and weak mutation approximation, I studied the average waiting time to parapatric speciation. The description of reproductive isolation used is based on the classical Dobzhansky model and its recently proposed multilocus generalizations. The dynamics of parapatric speciation are modelled as a biased random walk performed by the average genetic distance between the residents and immigrants. If a small number of genetic changes is sufficient for complete reproductive isolation, mutation and random genetic drift alone can cause speciation on the time-scale of ten to 1,000 times the inverse of the mutation rate over a set of loci underlying reproductive isolation. Even relatively weak selection for local adaptation can dramatically decrease the waiting time to speciation. The actual duration of the parapatric speciation process (that is the duration of intermediate forms in the actual transition to a state of complete reproductive isolation) is shorter by orders of magnitude than the overall waiting time to speciation. For a wide range of parameter values, the actual duration of parapatric speciation is of the order of one over the mutation rate. In general, parapatric speciation is expected to be triggered by changes in the environment.

Animals↗
PubMed2001

Rapid evolution of a sexual reproduction gene in centric diatoms of the genus Thalassiosira.

Sexual reproduction is commonly assumed to occur in the vast majority of diatoms due to the intimate association of this process with cell size control. Surprisingly, however, little is known about the impact of sexual events on diatom population dynamics. The Sig1 gene is strongly upregulated during sexual reproduction in the centric diatom Thalassiosira weissflogii and has been hypothesized to encode a protein involved in gamete recognition. In the present study, degenerate PCR primers were designed and used to amplify a portion of Sig1 from three closely related species in the cosmopolitan genus Thalassiosira, Thalassiosira oceanica, Thalassiosira guillardii, and Thalassiosira pseudonana. Identification of Sig1 in these three additional species facilitated development of this gene as a molecular marker for diatom sexual events. Examination of the new sequences indicated that multiple copies of Sig1 are probably present in the genome. Moreover, compared to the housekeeping gene beta-tubulin, the Sig1 genes of isolates of T. weissflogii collected from different regions of the Atlantic and Pacific oceans displayed high levels of divergence. The Sig1 genes of the four closely related Thalassiosira species also displayed high levels of sequence divergence compared to the levels observed with a second gene, Fcp, probably explaining why Sig1 could not be amplified from more distantly related species. The high levels of sequence divergence both within and between species suggest that Sig1 is rapidly evolving in a manner reminiscent of the manner observed in other genes that encode gamete recognition proteins. A simple model is presented for Sig1 evolution and the implications of such a rapidly evolving sexual reproduction gene for diatom speciation and population dynamics.

Amino Acid Sequence↗
PubMed2006

Allopolyploid origin of Cardamine asarifolia (Brassicaceae): incongruence between plastid and nuclear ribosomal DNA sequences solved by a single-copy nuclear gene.

Interspecific hybridization and polyploidization have played central roles in plant diversification. However, technical difficulties in the analyses of low-copy genes have limited the study of the origins of hybrid and polyploid plants. Here, we present a phylogenetic analysis of the hexaploid Cardamine asarifolia, distributed in the southern European Alps and northern Apennines. Our study included all relevant taxa of the genus found in Europe. A marked discrepancy was revealed between the trnL-trnF region of cpDNA and internal transcribed spacer (nrDNA ITS) sequences. To solve the incongruence, we sequenced a single-copy nuclear CHS gene (chalcone synthase) using a novel method to design homoeologue-specific PCR primers to bypass artefacts caused by artificial recombination of homoeologues during PCR and/or cloning. Three homoeologues were isolated from C. asarifolia, providing evidence for its allopolyploid origin. One homoeologue, showing the same phylogenetic position as the ITS sequences, most likely originated from an extinct parent. Furthermore, we documented recurrent polytopic hybridizations between C. asarifolia and diploid C. amara. The allohexaploidization and the following hybridization with a diploid species exemplify the ongoing dynamic processes of speciation in the genus Cardamine.

Acyltransferases↗
PubMed2003

Speciation in multidimensional evolutionary space.

Adaptive dynamics in two-dimensional phenotype space is investigated by computer simulation. The model assumes Lotka-Voltera-type competition and a stochastic mutation process. The carrying capacity has a single maximum in the origin of the strategy space and the competition coefficient decreases with strategy difference. Evolutionary branching, an asexual analog of adaptive speciation, is observed with suitable parameters. The branching at the singular point, which is a fixed point of the directional evolution, may occur into two or three, but not more, directions. Further branchings may occur after the initial separation. The probability of three-branching is studied as a function of several parameters. We conclude that the two-way branching is the predominant mode of adaptive speciation.

Adaptation, Physiological↗
PubMed2005

A systematic investigation of aluminium ion speciation at high temperature. Part 1. Solution studies.

Speciation diagrams of aluminium ions in aqueous solution (0.2 M) at high temperature (90 degrees C) have been obtained from 48 h time-resolved multi-batch titration experiments monitored by 27Al NMR spectroscopy, potentiometry and dynamic light scattering. The quantitative speciation patterns and kinetic data obtained offer a dynamic picture of the distribution of soluble and insoluble Al species as a function of hydrolysis ratio h(h=[OH-]/[Al3+]) over a very broad range of conditions (-1.0 < or =h < or = 4.0). Monomeric, small oligomeric, tridecameric (the 'Al13-mer') and the recently characterised 30-meric aluminium species (the 'Al30-mer') as well as aluminium hydroxide have been identified and quantified. The Al13-mer species dominates over a relatively broad range of hydrolysis ratios (1.5 < or =h< or = 2.7) during the first 6 h of experiment, but are gradually replaced by Al30-mers at longer reaction times. Kinetic profiles indicate that the formation of the Al30-mer is limited by the disappearance of the Al13 species at mildly acidic conditions. The estimated rate constants of both hydrolytic processes show good internal correlation at h> or = 1.5. The effect of local perturbations leading to the formation of aluminium hydroxide below the electroneutrality point (h= 3.0) has been estimated quantitatively.

Journal Article↗
PubMed2006

Will sympatric speciation fail due to stochastic competitive exclusion?

Sympatric speciation requires coexistence of the newly formed species. If divergence proceeds by small mutational steps, the new species utilize almost the same resources initially, and full speciation may be impeded by competitive exclusion in stochastic environments. We investigate this primarily ecological problem of sympatric speciation by studying the population dynamics of a diverging asexual population in a fluctuating environment. Correlation between species responses to environmental fluctuation is assumed to decrease with distance in trait space. Rapidly declining correlation in combination with high environmental variability may delay full speciation or even render it impossible. Stochastic extinctions impeding speciation are most likely when correlation decays faster than competition, for example, when demographic stochasticity is strong or when divergence is not accompanied by niche separation, such as in speciation driven entirely by sexual selection. Our general theoretical results show an interesting connection between short-term ecological dynamics and long-term, large-scale evolution.

Computer Simulation↗
PubMed2006

DNA barcoding will often fail to discover new animal species over broad parameter space.

With increasing force, genetic divergence of mitochondrial DNA (mtDNA) is being argued as the primary tool for discovery of animal species. Two thresholds of single-gene divergence have been proposed: reciprocal monophyly, and 10 times greater genetic divergence between than within species (the "10x rule"). To explore quantitatively the utility of each approach, we couple neutral coalescent theory and the classical Bateson-Dobzhansky-Muller (BDM) model of speciation. The joint stochastic dynamics of these two processes demonstrate that both thresholds fail to "discover" many reproductively isolated lineages under a single incompatibility BDM model, especially when BDM loci have been subject to divergent selection. Only when populations have been isolated for > 4 million generations did these thresholds achieve error rates of < 10% under our model that incorporates variable population sizes. The high error rate evident in simulations is corroborated with six empirical data sets. These properties suggest that single-gene, high-throughput approaches to discovering new animal species will bias large-scale biodiversity surveys, particularly toward missing reproductively isolated lineages that have emerged by divergent selection or other mechanisms that accelerate reproductive isolation. Because single-gene thresholds for species discovery can result in substantial error at recent divergence times, they will misrepresent the correspondence between recently isolated populations and reproductively isolated lineages (= species).

Animals↗
PubMed1997

Genome plasticity as a paradigm of eubacteria evolution.

To test the hypotheses that eubacterial genomes leave evolutionarily stable structures and that the variety of genome size is brought about through genome doubling during evolution, the genome structures of Haemophilus influenzae, Mycoplasma genitalium, Escherichia coli, and Bacillus subtilis were compared using the DNA sequences of the entire genome or substantial portions of genome. In these comparisons, the locations of orthologous genes were examined among different genomes. Using orthologous genes for the comparisons guaranteed that differences revealed in physical location would reflect changes in genome structure after speciation. We found that dynamic rearrangements have so frequently occurred in eubacterial genomes as to break operon structures during evolution, even after the relatively recent divergence between E. coli and H. influenzae. Interestingly, in such eubacterial genomes of high plasticity, we could find several highly conservative regions with the longest conserved region comprising the S10, spc, and alpha operons. This suggests that such exceptional conservative regions have undergone strong structural constraints during evolution.

Bacteria↗
PubMed2006

Short-term dynamic change of gill copper in common carp, Cyprinus carpio, evaluated by a sequential extraction.

Dynamic changes in Cu speciation and its binding to fish gills were investigated by exposing common carp (Cyprinus carpio) to a 1 mg/1 Cu solution for 7 hours. Cu speciation in the bulk solution and fish gill microenvironment was calculated using general chemical equilibrium modeling. A sequential extraction procedure using distilled water, magnesium dichloride (1.0 mol/1), and acetic acid (10%) was used to characterize the Cu associated with the fish gills. Cu residual in the gill tissue was measured after the sequential extraction. Changes in total Cu concentration, pH, and dissolved organic carbon (Doc) in the bulk solution were recorded during the experimental period and calculated for the fish gill microenvironment. Cu-hydroxide species and Cu2 were dominant Cu species in both bulk solution and the fish gill microenvironment, whereas increased Cu-mucus was found in the fish gill microenvironment. DOC in the exposure medium, assumed to arise from mucus release, also increased and complexed Cu in solution. Forty-three percent of the Cu associated with the gills was readily water extractable, with an additional 22% exchangeable with Mg2+ or protons. Only 35% of the Cu accumulated within the gill tissues. The binding of Cu to the fish gills reached apparent equilibrium after 3 hours of exposure. Furthermore, the amount of water-extractable Cu within the gills showed significant correlation to the concentration of Cu predicted to be complexed with calculated free mucus in the gill microenvironment.

Animals↗
PubMed2005

Modelling dewatering behaviour through an understanding of solids formation processes. Part I--Solids formation considerations.

An understanding of the mechanisms which control solids formation can provide information on the characteristics of the solids which are formed. These characteristics will in turn impact on dewatering behaviour. In this paper a model for solids formation is proposed. The first part of the model considers the hydrodynamics in the precipitation vessel, from which a reactant mixing model is developed. Spatially variant solution conditions are quantified (dynamically) using an equilibrium speciation model. These calculations are performed in conjunction with an adsorption model, accounting for equilibria involving adsorbed species. The kinetics of solids formation, including nucleation, growth and aggregation, are described empirically using spatially variant supersaturation profiles. These, together with moment transformations of the solids population balance, describe the evolution of particle sizes throughout the precipitation process. Precipitation of nickel hydroxide is explored experimentally, and models developed are fitted to the results. Comments are offered on the impact of simplifications required for computational reasons, and assumptions required due to lack of information, on the accuracy of the model. In part II of this paper, the use of model outputs in predicting filtration behaviour is explored.

Adsorption↗
PubMed2004

Molecular phylogeny and biogeography of the dung beetle genus Temnoplectron Westwood (Scarabaeidae: Scarabaeinae) from Australia's wet tropics.

The landscape of the Australian Wet Tropics can be described as "islands" of montane rainforest surrounded by warmer or more xeric habitats. Historical glaciation cycles have caused expansion and contraction of these rainforest "islands" leading to consistent patterns of genetic divergence within species of vertebrates. To explore whether this dynamic history has promoted speciation in endemic and diverse groups of insects, we used a combination of mtDNA sequencing and morphological characters to estimate relationships and the tempo of divergence among Australian representatives of the dung beetle genus Temnoplectron. This phylogenetic hypothesis shares a number of well-supported clades with a previously published phylogenetic hypothesis based on morphological data, though statistical support for several nodes is weak. Sister species relationships well-supported in both tree topologies, and a tree obtained by combining the two data sets, suggest that speciation has mostly been allopatric. We identify a number of speciation barriers, which coincide with phylogeographic breaks found in vertebrate species. Large sequence divergences between species emphasize that speciation events are ancient (pre-Pleistocene). The flightless, rainforest species appear to have speciated rapidly, but also in the distant past.

Animals↗
PubMed2002

Manganese oxidation state and its implications for toxicity.

Manganese (Mn) is ubiquitous in mammalian systems and is essential for proper development and function, though it can also be toxic at elevated exposures. While essential biologic functions of Mn depend on its oxidation state [e.g., Mn(II), Mn(III)], little is known about how the oxidation state of elevated Mn exposures affect cellular uptake, and function/toxicity. Here we report the dynamics of EPR measurable Mn(II) in fresh human plasma and cultured PC12 cell lysates as a function of exposure to either manganese(II) chloride or manganese(III) pyrophosphate, and the effects of exposure to Mn(II) versus Mn(III) on total cellular aconitase activity and cellular Mn uptake. The results indicate that Mn(II) or Mn(III) added in vitro to fresh human plasma or cell lysates yielded similar amounts of EPR measurable Mn(II). In contrast, Mn added as Mn(III) was significantly more effective in inhibiting total cellular aconitase activity, and intact PC12 cells accumulated significantly more Mn when exposures occurred as Mn(III). Collectively, these data reflect the dynamic nature of Mn speciation in simple biological systems, and the importance of Mn oxidation/speciation state in mediating potential cellular toxicity. This study supports concern over increased environmental exposures to Mn in different oxidation states [Mn(II), Mn(III), and Mn(IV)] that may arise from combustion products of the gasoline antiknock additive methycyclopentadienyl manganese tricarbonyl (MMT).

Aconitate Hydratase↗