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At least 541 records · Page 30Linked to original sources
PubMed2006

Absence of phylogenetic signal in the niche structure of meadow plant communities.

A significant proportion of the global diversity of flowering plants has evolved in recent geological time, probably through adaptive radiation into new niches. However, rapid evolution is at odds with recent research which has suggested that plant ecological traits, including the beta- (or habitat) niche, evolve only slowly. We have quantified traits that determine within-habitat alpha diversity (alpha niches) in two communities in which species segregate on hydrological gradients. Molecular phylogenetic analysis of these data shows practically no evidence of a correlation between the ecological and evolutionary distances separating species, indicating that hydrological alpha niches are evolutionarily labile. We propose that contrasting patterns of evolutionary conservatism for alpha- and beta-niches is a general phenomenon necessitated by the hierarchical filtering of species during community assembly. This determines that species must have similar beta niches in order to occupy the same habitat, but different alpha niches in order to coexist.

Base Sequence↗
PubMed2006

A newly recognized fossil coelacanth highlights the early morphological diversification of the clade.

Previously considered an actinopterygian or an osteichthyan incertae sedis, the Devonian (Givetian-Frasnian) Holopterygius nudus is reinterpreted as a coelacanth. This genus is among the oldest coelacanths known from articulated remains, but its eel-like morphology marks a considerable departure from the conventional coelacanth body plan. A cladistic analysis places Holopterygius as the sister taxon of the Carboniferous (Serpukhovian) genus Allenypterus. Despite the specialized morphology of these genera, they occupy a surprisingly basal position in coelacanth phylogeny; only Diplocercides and Miguashaia are further removed from the crown. A morphometric analysis reveals that coelacanths were anatomically disparate early in their history. Conflicts between this result and those of previous studies challenge the adequacy of systematic character sets for describing historical patterns of morphological variety. Coelacanths have long had an iconic place in the study of vertebrate evolution for their apparent anatomical conservatism over geological time, but Holopterygius provides clear evidence for rapid morphological evolution early in the history of this clade.

Animals↗
PubMed2006

Rapid lineage accumulation in a non-adaptive radiation: phylogenetic analysis of diversification rates in eastern North American woodland salamanders (Plethodontidae: Plethodon).

Adaptive radiations have served as model systems for quantifying the build-up of species richness. Few studies have quantified the tempo of diversification in species-rich clades that contain negligible adaptive disparity, making the macroevolutionary consequences of different modes of evolutionary radiation difficult to assess. We use mitochondrial-DNA sequence data and recently developed phylogenetic methodologies to explore the tempo of diversification of eastern North American Plethodon, a species-rich clade of woodland salamanders exhibiting only limited phenotypic disparity. Lineage-through-time analysis reveals a high rate of lineage accumulation, 0.8 species per million years, occurring 11-8 million years ago in the P. glutinosus species group, followed by decreasing rates. This high rate of lineage accumulation is exceptional, comparable to the most rapid of adaptive radiations. In contrast to classic models of adaptive radiation where ecological niche divergence is linked to the origin of species, we propose that phylogenetic niche conservatism contributes to the rapid accumulation of P. glutinosus-group lineages by promoting vicariant isolation and multiplication of species across a spatially and temporally fluctuating environment. These closely related and ecologically similar lineages persist through long-periods of evolutionary time and form strong barriers to the geographic spread of their neighbours, producing a subsequent decline in lineage accumulation. Rapid diversification among lineages exhibiting long-term maintenance of their bioclimatic niche requirements is an under-appreciated phenomenon driving the build-up of species richness.

Animals↗
PubMed2006

Historical processes enhance patterns of diversity along latitudinal gradients.

One of the more vexing issues in ecology is how historical processes affect contemporary patterns of biodiversity. Accordingly, few models have been presented. Two corollary models (centre of origin, time-for-speciation) can be used to make quantitative predictions characterizing the tropical niche conservatism hypothesis and describe diversification as diffusion and subsequent cladogenesis of species away from the place of origin of a higher taxon in the tropics. Predictions derived from such models are: (i) species richness declines toward the periphery of the range of a higher taxon; (ii) taxa are more derived toward the periphery than the centre; (iii) ages of taxa are lower toward the periphery than the centre; and (iv) ages and measures of derivedness are less variable toward the periphery of the range of a higher taxon. I tested these predictions to better understand the formation of one of the most ubiquitous patterns of biodiversity-the latitudinal gradient in species richness. Results indicate well-supported predictions for New World leaf-nosed bats and that diversification has had strong influences on latitudinal gradients of species richness. A better understanding of how evolutionary diversification of taxa contributes to formation of patterns of species richness along environmental gradients is necessary to fully understand spatial variation in biodiversity.

Animals↗
PubMed2007

Learning the ecological niche.

A cornerstone of ecological theory is the ecological niche. Yet little is known about how individuals come to adopt it: whether it is innate or learned. Here, we report a cross-fostering experiment in the wild where we transferred eggs of blue tits, Cyanistes caeruleus, to nests of great tits, Parus major, and vice versa, to quantify the consequences of being reared in a different social context, but in an environment otherwise natural to the birds. We show that early learning causes a shift in the feeding niche in the direction of the foster species and that this shift lasts for life (foraging conservatism). Both species changed their feeding niches, but the change was greater in the great tit with its less specialized feeding behaviour. The study shows that cultural transmission through early learning is fundamental to the realization of ecological niches, and suggests a mechanism to explain learned habitat preference and sympatric speciation in animals.

Animals↗
PubMed2001

Reconstructing the origins of human hepatitis viruses.

Infections with hepatitis B and C viruses (HBV, HCV) are widespread in human populations throughout the world, and are major causes of chronic liver disease and liver cancer. HBV, HCV and the related hepatitis G virus or GB virus C (referred to here as HGV/GBV-C) are capable of establishing persistent, frequently lifelong infections characterized by high levels of continuous replication. All three viruses show substantial genetic heterogeneity, which has allowed each to be classified into a number of distinct genotypes that have different geographical distributions and associations with different risk groups for infection. Information on their past transmission and epidemiology might be obtained by estimation of the time of divergence of the different genotypes of HCV, HBV and HGV/GBV-C using knowledge of their rates of sequence change. While information on the latter is limited to short observation periods and is therefore subject to considerable error and uncertainty, the relatively recent times of origin for genotype of each virus predicted by this method (HCV, 500-2000 years; HBV, 3000 years; HGV/GBV-C, 200 years) are quite incompatible with their epidemiological distributions in human populations. They also cannot easily be reconciled with the recent evidence for species-associated variants of HBV and HGV/GBV-C in a range of non-human primates. The apparent conservatism of viruses over long periods implied by their epidemiological distributions instead suggests that nucleotide sequence change may be subject to constraints peculiar to viruses with single-stranded genomes, or with overlapping reading frames that defy attempts to reconstruct evolution according to the principles of the 'molecular clock'. Large population sizes and intense selection pressures that optimize fitness may be additional factors that set virus evolution apart from that of their hosts.

Animals↗
PubMed2001

The origin and evolution of hepatitis viruses in humans.

The spread and origins of hepatitis C virus (HCV) in human populations have been the subject of extensive investigations, not least because of the importance this information would provide in predicting clinical outcomes and controlling spread of HCV in the future. However, in the absence of historical and archaeological records of infection, the evolution of HCV and other human hepatitis viruses can only be inferred indirectly from their epidemiology and by genetic analysis of contemporary virus populations. Some information on the history of the latter may be obtained by dating the time of divergence of various genotypes of HCV, hepatitis B virus (HBV) and the non-pathogenic hepatitis G virus (HGV)/GB virus-C (GBV-C). However, the relatively recent times predicted for the origin of these viruses fit poorly with their epidemiological distributions and the recent evidence for species-associated variants of HBV and HGV/GBV-C in a wide range of non-human primates. The apparent conservatism of viruses over long periods implied by these latter observations may be the result of constraints on sequence change peculiar to viruses with single-stranded genomes, or with overlapping reading frames. Large population sizes and intense selection pressures that optimize fitness may be the factors that set virus evolution apart from that of their hosts.

Amino Acid Sequence↗
PubMed2004

Genetic diversity and evolution of hepatitis C virus--15 years on.

In the 15 years since the discovery of hepatitis C virus (HCV), much has been learned about its role as a major causative agent of human liver disease and its ability to persist in the face of host-cell defences and the immune system. This review describes what is known about the diversity of HCV, the current classification of HCV genotypes within the family Flaviviridae and how this genetic diversity contributes to its pathogenesis. On one hand, diversification of HCV has been constrained by its intimate adaptation to its host. Despite the >30 % nucleotide sequence divergence between genotypes, HCV variants nevertheless remain remarkably similar in their transmission dynamics, persistence and disease development. Nowhere is this more evident than in the evolutionary conservation of numerous evasion methods to counteract the cell's innate antiviral defence pathways; this series of highly complex virus-host interactions may represent key components in establishing its 'ecological niche' in the human liver. On the other hand, the mutability and large population size of HCV enables it to respond very rapidly to new selection pressures, manifested by immune-driven changes in T- and B-cell epitopes that are encountered on transmission between individuals with different antigen-recognition repertoires. If human immunodeficiency virus type 1 is a precedent, future therapies that target virus protease or polymerase enzymes may also select very rapidly for antiviral-resistant mutants. These contrasting aspects of conservatism and adaptability provide a fascinating paradigm in which to explore the complex selection pressures that underlie the evolution of HCV and other persistent viruses.

Biological Evolution↗
PubMed2004

Reliable LQ fuzzy control for continuous-time nonlinear systems with actuator faults.

This paper deals with the reliable linear quadratic (LQ) fuzzy control problem for continuous-time nonlinear systems with actuator faults. The Takagi-Sugeno (T-S) fuzzy model is employed to represent a nonlinear system. By using multiple Lyapunov functions, an improved linear matrix inequality (LMI) method for the design of reliable LQ fuzzy controllers is investigated, which reduces the conservatism of using a single Lyapunov function. The different upper bounds on the LQ performance cost function for the normal and different actuator fault cases are provided. A suboptimal reliable LQ fuzzy controller is given by means of an LMI optimization procedure, which can not only guarantee the stability of the closed-loop overall fuzzy system for all cases, but also provide an optimized upper bound on a weighted average LQ performance cost function. Finally, numerical simulations on the chaotic Lorenz system are given to illustrate the application of the proposed design method.

Algorithms↗
PubMed2006

Robust H infinity static output feedback control of fuzzy systems: an ILMI approach.

This paper examines the problem of robust H infinity static output feedback control of a Takagi-Sugeno fuzzy system. The proposed robust H infinity static output feedback controller guarantees the pounds 2 gain of the mapping from the exogenous disturbances to the regulated output to be less than or equal to a prescribed level. The existence of a robust H infinity static output feedback control is given in terms of the solvability of bilinear matrix inequalities. An iterative algorithm based on the linear matrix inequality is developed to compute robust H infinity static output feedback gains. To reduce the conservatism of the design, the structural information of membership function characteristics is incorporated. A numerical example is used to illustrate the validity of the design methodologies.

Algorithms↗
PubMed2002

Risk and uncertainty analysis in government safety decisions.

Probabilistic risk analysis (PRA) can be an effective tool to assess risks and uncertainties and to set priorities among safety policy options. Based on systems analysis and Bayesian probability, PRA has been applied to a wide range of cases, three of which are briefly presented here: the maintenance of the tiles of the space shuttle, the management of patient risk in anesthesia, and the choice of seismic provisions of building codes for the San Francisco Bay Area. In the quantification of a risk, a number of problems arise in the public sector where multiple stakeholders are involved. In this article, I describe different approaches to the treatments of uncertainties in risk analysis, their implications for risk ranking, and the role of risk analysis results in the context of a safety decision process. I also discuss the implications of adopting conservative hypotheses before proceeding to what is, in essence, a conditional uncertainty analysis, and I explore some implications of different levels of "conservatism" for the ranking of risk mitigation measures.

Journal Article↗
PubMed2002

Assessing human health response in life cycle assessment using ED10s and DALYs: part 2--Noncancer effects.

In Part 1 of this article we developed an approach for the calculation of cancer effect measures for life cycle assessment (LCA). In this article, we propose and evaluate the method for the screening of noncancer toxicological health effects. This approach draws on the noncancer health risk assessment concept of benchmark dose, while noting important differences with regulatory applications in the objectives of an LCA study. We adopt the centraltendency estimate of the toxicological effect dose inducing a 10% response over background, ED10, to provide a consistent point of departure for default linear low-dose response estimates (betaED10). This explicit estimation of low-dose risks, while necessary in LCA, is in marked contrast to many traditional procedures for noncancer assessments. For pragmatic reasons, mechanistic thresholds and nonlinear low-dose response curves were not implemented in the presented framework. In essence, for the comparative needs of LCA, we propose that one initially screens alternative activities or products on the degree to which the associated chemical emissions erode their margins of exposure, which may or may not be manifested as increases in disease incidence. We illustrate the method here by deriving the betaED10 slope factors from bioassay data for 12 chemicals and outline some of the possibilities for extrapolation from other more readily available measures, such as the no observable adverse effect levels (NOAEL), avoiding uncertainty factors that lead to inconsistent degrees of conservatism from chemical to chemical. These extrapolations facilitated the initial calculation of slope factors for an additional 403 compounds; ranging from 10(-6) to 10(3) (risk per mg/kg-day dose). The potential consequences of the effects are taken into account in a preliminary approach by combining the betaED10 with the severity measure disability adjusted life years (DALY), providing a screening-level estimate of the potential consequences associated with exposures, integrated over time and space, to a given mass of chemical released into the environment for use in LCA.

Dose-Response Relationship, Drug↗
PubMed2025

A Functionally Conserved yet Dynamically Evolving Toolkit Underpinning Molluscan Biomineralization: Insights From Shell and Radula.

The molluscan shell and radula constitute pivotal molluscan innovations, each characterized by distinct functions and diverse forms, regulated by the highly specific biomineralization regulatory networks. Despite their paramount importance, the conserved components and adaptive evolutionary processes governing these regulatory networks remain unresolved. To address this knowledge gap, we advocate for the integration of data from less-explored lineages, such as Scaphopoda, as an essential step. This study presents the inaugural comprehensive transcriptome analysis of Pictodentalium vernedei, a representative species of Scaphopoda distinguished by a unique and evolutionarily conserved shell morphology and radula structure. Furthermore, comparative transcriptome/genome analyses are employed to unravel the conservatism and evolutionary innovation of the involved biomineralization regulatory elements. Our findings underscore the central role of secretomes in governing biomineralization processes, and we identified a fundamental set of 26 domains within molluscan secretomes, forming an essential functional protein domain repertoire necessary for the transformation of inorganic ions into biomineralized structures. This core biomineralization toolkit has undergone independent expansion and lineage-specific recruitment, giving rise to novel, modular domain architectures. This may be essential for the functional specialization and morphological diversification of shell and radula structures. These evolutionary processes are driven by the independent co-option of ancient genes and the emergence of novel de novo genes. This comprehensive investigation not only contributes insights into the evolution of molluscan biomineralization structures but also establishes avenues for further scholarly exploration.

Animals↗
PubMed2001

Body size variation among mainland populations of the western rattlesnake (Crotalus viridis).

In general, squamate reptiles follow the converse to Bergmann's rule, attaining smaller sizes in cooler environments, whereas other vertebrate groups follow Bergmann's rule, attaining larger sizes in cooler areas. Intensive studies of body size evolution for species of squamates are necessary to understand the processes responsible for this trend. Here I present data on body size variation among mainland populations of the western rattlesnake, Crotalus viridis. This species consists of two well-differentiated phylogenetic clades, therefore all analyses were performed for the C. viridis group as a whole and separately for each of the two clades within the C. viridis group. Although both phylogenetic and nonphylogenetic analyses were performed, the data did not show phylogenetic conservatism, and therefore the nonphylogenetic results are preferred. I found no significant relationships between mean adult female snout-vent length and any of the physical and climatic variables that were examined for the C. viridis group using simple linear regression analysis. Examined separately, I found that individuals of the western clade, C. oreganus, were smaller in cooler and more seasonal environments, whereas individuals of the eastern clade. C. viridis sensu stricto, were larger in cooler and more seasonal areas. Thus, the observed size trends were in opposite directions for the two clades. Multiple regression analysis revealed that seasonality was a stronger predictor of body size variation than was temperature for both clades. The differences in body size trends between these clades may be due to differences in mortality rates among populations.

Animals↗
PubMed2002

Transition rates between specialization and generalization in phytophagous insects.

Although most species of animals exhibit specialized patterns of resource use, it is unclear whether specialization evolves at a faster rate than generalization. To test this hypothesis, transition rates toward specialization and toward generalization were estimated using phylogenies from 15 groups of phytophagous insects. Among the groups studied, maximum-likelihood analyses showed that the forward transition rate from generalization to specialization was significantly higher than the reverse transition rate from specialization to generalization (mean ratio of forward to reverse transition rate = 1.47 using uniform branch lengths and 1.76 using Grafen branch lengths). Although phylogenetic conservatism of host-plant use is common, the results suggest that the evolution of specialization is a highly dynamic process. For example, higher transitions rates both toward and away from specialization as well as equal transition rates were inferred. Collectively, the results reveal a tendency for directional evolution toward increased specialization but also indicate that specialization does not always represent an evolutionary dead-end that strongly limits further evolution.

Animals↗
PubMed2003

Phylogeographic structure and cryptic speciation in the trans-Antarctic moss Pyrrhobryum mnioides.

Many bryophyte species have distributions that span multiple continents. The hypotheses historically advanced to explain such distributions rely on either long-distance spore dispersal or slow rates of morphological evolution following ancient continental vicariance events. We use phylogenetic analyses of DNA sequence variation at three chloroplast loci (atpB-rbcL spacer, rps4 gene, and trnL intron and 3' spacer) to examine these two hypotheses in the trans-Antarctic moss Pyrrhobryum mnioides. We find: (1) reciprocal monophyly of Australasian and South American populations, indicating a lack of intercontinental dispersal; (2) shared haplotypes between Australia and New Zealand, suggesting recent or ongoing migration across the Tasman Sea; and (3) reciprocal monophyly among Patagonian and neotropical populations, suggesting no recent migration along the Andes. These results corroborate experimental work suggesting that spore features may be critical determinants of species range. We use the mid-Miocene development of the Atacama Desert, 14 million years ago, to calibrate a molecular clock for the tree. The age of the trans-Antarctic disjunction is estimated to be 80 million years ago, consistent with Gondwanan vicariance, making it among the most ancient documented cases of cryptic speciation. These data are in accord with niche conservatism, but whether the morphological stasis is a product of stabilizing selection or phylogenetic constraint is unknown.

Antarctic Regions↗
PubMed2003

Quantifying phylogenetically structured environmental variation.

Comparative analysis methods control for the variation linked to phylogeny before attempting to correlate the remaining variation of a trait to present-day conditions (i.e., ecology and/or environment). A portion of the phylogenetic variation of the trait may be related to ecology, however; this portion is called "phylogenetic niche conservatism." We propose a method of variation partitioning that allows users to quantify this portion of the variation, called the "phylogenetically structured environmental variation." The new method is applied to published data to study, in a phylogenetic framework, the link between body mass and population density in 79 species of mammals. The results suggest that an important part of the variation of mammal body mass is related to the common influence of phylogeny and population density.

Analysis of Variance↗
PubMed2004

The vulvar epithelium differs from the skin: implications for cutaneous testing to address topical vulvar exposures.

Vulvar tissue is more permeable than exposed skin due to differences in structure, occlusion, hydration and susceptibility to friction. The safety assessment of products that contact the vulva should account for this potentially heightened permeability. Standard clinical patch tests may not sufficiently mimic vulvar exposures. Because testing on the vulva is not routinely feasible, we are investigating new and modified cutaneous test methods to increase the degree of conservatism of the safety assessment. To this end, we have 1) developed a method to assess chemical and frictional effects by means of repeated application to the popliteal fossa (the behind-the-knee test); 2) modified the quantitative risk assessment for the induction of allergic contact dermatitis; and 3) proposed a modified human repeat insult patch test for assessing materials intended for vulvar contact. Modification of the traditional 4-day, irritation patch test by using wet samples or compromized skin sites failed to enhance test sensitivity. Future studies will evaluate testing in subjects with heightened susceptibility to chemical and sensory irritation, in order to increase test sensitivity to chemical irritants. These approaches can be employed to augment the margin of safety when cutaneous test methods are applied to agents that contact the vulva.

Dermatitis, Allergic Contact↗