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PubMed2004

Egg size evolution in tropical American arcid bivalves: the comparative method and the fossil record.

Marine organisms exhibit a wide range of egg sizes, even among closely related taxa, and egg size is widely considered to be one of the most important components of the life histories of marine species. The nature of the trade-off between egg size and number and the consequences of variation in egg size for offspring growth and survivorship have been extensively modeled. Yet, there is little empirical evidence that supports the relative importance of particular environmental parameters in engendering the tremendous variation in egg size seen in marine organisms. This study compares egg sizes between six geminate species pairs of bivalves in the family Arcidae to determine whether egg size differs in predictable directions between geminate species in the two oceans separated by the Central American isthmus, and whether the direction and timing of egg size evolution among geminates in this family is correlated with both modern and paleoceanographic patterns of oceanic productivity. In all modern members of six geminate pairs, egg size was larger in the species in the western Atlantic than in its sister species the eastern Pacific. This pattern supports the hypothesis that optimal egg size differs in the two oceans due to the low productivity and poor larval feeding environment in the western Atlantic relative to the eastern Pacific. The fossil record of one geminate pair shows that egg size has remained consistently large in the western Atlantic from the Miocene to the Recent, while egg size in the eastern Pacific has decreased to the current small size in less than 2 million years; this suggests that modern-day differences between egg sizes in the western Atlantic and eastern Pacific are due to either an increase in productivity in the eastern Pacific and subsequent selection for smaller eggs in that ocean, or differential patterns of extinction that occurred well after the rise of the isthmus. These results agree with ancestral character state reconstruction using linear parsimony, but differ from squared-change parsimony reconstructions.

Animals↗

PubMed2006

Laonastes and the "Lazarus effect" in recent mammals.

The living Laotian rodent Laonastes aenigmamus, first described in early 2005, has been interpreted as the sole member of the new family Laonastidae on the basis of its distinctive morphology and apparent phylogenetic isolation from other living rodents. Here we show that Laonastes is actually a surviving member of the otherwise extinct rodent family Diatomyidae, known from early Oligocene to late Miocene sites in Pakistan, India, Thailand, China, and Japan. Laonastes is a particularly striking example of the "Lazarus effect" in Recent mammals, whereby a taxon that was formerly thought to be extinct is rediscovered in the extant biota, in this case after a temporal gap of roughly 11 million years.

Animals↗

PubMed2000

Recovery and management options for spring/summer chinook salmon in the Columbia River basin.

Construction of four dams on the lower Snake River (in northwestern United States) between 1961 and 1975 altered salmon spawning habitat, elevated smolt and adult migration mortality, and contributed to severe declines of Snake River salmon populations. By applying a matrix model to long-term population data, we found that (i) dam passage improvements have dramatically mitigated direct mortality associated with dams; (ii) even if main stem survival were elevated to 100%, Snake River spring/summer chinook salmon (Oncorhynchus tshawytscha) would probably continue to decline toward extinction; and (iii) modest reductions in first-year mortality or estuarine mortality would reverse current population declines.

Animals↗

PubMed1983

Front dentition of the omomyiformes (Primates).

Within the primates the front dentition plays a major role in the classification of the different taxa. The extant strepsirhines are clearly characterized by the possession of a tooth comb. Tarsius differs in this complex by a construction which remembers the beak of an owl (vertically implanted medial incisors, upper pair bigger than mandibular pair). The front teeth of the extinct Microchoeridae are described. The dental formula of the group is discussed and compared with the Omomyidae. The wear pattern presents evidence of a dental comb as early as the Late Eocene.

Animals↗

PubMed2006

Imperfect vaccines and the evolution of pathogens causing acute infections in vertebrates.

A study by Gandon et al. (2001) considered the potential ways pathogens may evolve in response to vaccination with imperfect vaccines. In this paper, by focusing on acute infections of vertebrate hosts, we examine whether imperfect vaccines that do not completely block a pathogen's replication (antigrowth) or transmission (antitransmission) may lead to evolution of more or less virulent pathogen strains. To address this question, we use models of the within-host dynamics of the pathogen and the host's immune responses. One advantage of the use of this within-host approach is that vaccination can be easily incorporated in the models and the trade-offs between pathogen transmissibility, host recovery, and virulence that drive evolution of pathogens in these models can be easily estimated. We find that the use of either antigrowth or antitransmission vaccines leads to the evolution of pathogens with an increased within-host growth rate; infection of unvaccinated hosts with such evolved pathogens results in high host mortality and low pathogen transmission. Vaccination of only a fraction of hosts with antigrowth vaccines may prevent pathogens from evolving high virulence due to pathogen adaptation to unvaccinated hosts and thus protection of vaccinated hosts from pathogen-induced disease. In contrast, antitransmission vaccines may be beneficial only if they are effective enough to cause pathogen extinction. Our results suggest that particular mechanisms of action of vaccines and their efficacy are crucial in predicting longterm evolutionary consequences of the use of imperfect vaccines.

Animal Diseases↗

PubMed2005

A mechanistic approach for modeling temperature-dependent consumer-resource dynamics.

Paramount to our ability to manage and protect biological communities from impending changes in the environment is an understanding of how communities will respond. General mathematical models of community dynamics are often too simplistic to accurately describe this response, partly to retain mathematical tractability and partly for the lack of biologically pleasing functions representing the model/environment interface. We address these problems of tractability and plausibility in community/environment models by incorporating the Boltzmann factor (temperature dependence) in a bioenergetic consumer-resource framework. Our analysis leads to three predictions for the response of consumer-resource systems to increasing mean temperature (warming). First, mathematical extinctions do not occur with warming; however, stable systems may transition into an unstable (cycling) state. Second, there is a decrease in the biomass density of resources with warming. The biomass density of consumers may increase or decrease depending on their proximity to the feasibility (extinction) boundary. Third, consumer biomass density is more sensitive to warming than resource biomass density (with some exceptions). These predictions are in line with many current observations and experiments. The model presented and analyzed here provides an advancement in the testing framework for global change scenarios and hypotheses of latitudinal and elevational species distributions.

Animals↗

PubMed2005

Semisynthesis and biological activity of aminoacyl triesters of squamocin, an annonaceous acetogenin.

A number of aminoacyl triesters of squamocin 1, a cytotoxic acetogenin isolated from the seeds of Annona reticulata, have been synthesized in two to three steps from protected (l)-aminoacids and squamocin 1 using standard coupling/deprotection procedures. These semisynthetic analogs were tested on submitochondrial particles (SMP) for their complex I inhibitory activities, and against KB 3-1 cells in vitro. All triesters derivatives exhibited a complete extinction of activity at the enzymatic level, correlated to a reduced though modulated cytotoxicity in comparison with squamocin 1. This activity can apparently be considered as a function of the amphipathy of the analogs, the more amphiphilic ones being the more cytotoxic.

Annona↗

PubMed2003

The evolutionary inheritance of elemental stoichiometry in marine phytoplankton.

Phytoplankton is a nineteenth century ecological construct for a biologically diverse group of pelagic photoautotrophs that share common metabolic functions but not evolutionary histories. In contrast to terrestrial plants, a major schism occurred in the evolution of the eukaryotic phytoplankton that gave rise to two major plastid superfamilies. The green superfamily appropriated chlorophyll b, whereas the red superfamily uses chlorophyll c as an accessory photosynthetic pigment. Fossil evidence suggests that the green superfamily dominated Palaeozoic oceans. However, after the end-Permian extinction, members of the red superfamily rose to ecological prominence. The processes responsible for this shift are obscure. Here we present an analysis of major nutrients and trace elements in 15 species of marine phytoplankton from the two superfamilies. Our results indicate that there are systematic phylogenetic differences in the two plastid types where macronutrient (carbon:nitrogen:phosphorus) stoichiometries primarily reflect ancestral pre-symbiotic host cell phenotypes, but trace element composition reflects differences in the acquired plastids. The compositional differences between the two plastid superfamilies suggest that changes in ocean redox state strongly influenced the evolution and selection of eukaryotic phytoplankton since the Proterozoic era.

Biological Evolution↗

PubMed2004

Neglected taxonomy of rare desert fishes: congruent evidence for two species of leatherside chub.

Conservation biologists rely heavily on taxonomy to set the scope for biological monitoring and recovery planning of rare or threatened species. Yet, taxonomic boundaries are seldom evaluated as falsifiable hypotheses that can be statistically tested. Here, we examine species boundaries in leatherside chub (Teleostei, Cyprinidae), an imperiled desert fish native to the Bonneville Basin and upper Snake River drainages of western North America. Recent molecular data hint that this fish could be composed of two distinct taxa that are geographically separated into northern and southern species. To formally test this hypothesis, we evaluated leatherside chub using several different categories of species concepts, including criteria dependent on phylogenetic, morphological, and ecological data. We found that leatherside chub is composed of two reciprocally monophyletic clades (candidate species) characterized by numerous fixed genetic differences for both mitochondrial and nuclear DNA markers; mtDNA sequence divergence between the two clades approached 8%. The candidate species also showed significant differences in cranial shape, revealed by morphometric analysis. Finally, controlled growth and foraging experiments using representative populations from each clade show that candidate species appear to be locally adapted to the thermal environments where they now occur. Combined, these three lines of evidence support the hypothesis that leatherside chub is composed of two species. Moreover, all lines of evidence place these two species within the genusLepidomeda, a group consisting of three additional species of endangered spinedace fishes, and one extinct species, all native to the Colorado River system. Hence, we elevate the two clades of leatherside chub to distinct species status (Lepidomeda copeiin the north andL. aliciaein the south), and argue that each warrants independent conservation and recovery action.

Animals↗

PubMed2004

Microbial structural diversity estimated by dilution-extinction of phenotypic traits and T-RFLP analysis along a land-use intensification gradient.

The present work tested whether the relationship between functional traits and inoculum density reflected structural diversity in bacterial communities from a land-use intensification gradient applying a mathematical model. Terminal restriction fragment length polymorphism (T-RFLP) analysis was also performed to provide an independent assessment of species richness. Successive 10-fold dilutions of a soil suspension were inoculated onto Biolog GN(R) microplates. Soil bacterial density was determined by total cell and plate counts. The relationship between phenotypic traits and inoculum density fit the model, allowing the estimation of maximal phenotypic potential (Rmax) and inoculum density (KI) at which Rmax will be half-reduced. Though Rmax decreased with time elapsed since clearing of native vegetation, KI remained high in two of the disturbed sites. The genetic pool of bacterial community did not experience a significant reduction, but the active fraction responding in the Biolog assay was adversely affected, suggesting a reduction in the functional potential.

Bacteria↗

PubMed1977

Biochemical, biophysical, and biological properties of densonucleosis virus (paravovirus). II. Two types of infectious virions.

Among the infectious densonucleosis virus (DNV) particles, two types of virions, DNV-I and DNV-II, have been identified. The density of DNV-I was about 1.40 g/ml and depended on the pH, whereas the density of DNV-II was independent of the pH and was 1.44 g/ml. The sedimentation rates of these particles were 111S and 89S, respectively. The specific extinction coefficients and the absorption spectra, corrected for light scattering, were also different for these two types. The electrophoretic mobility of both types of virions was identical under the experimental conditions used. Both types of particles contained single-stranded DNA with similar physicochemical properties. The difference between these types of virions seemed to be due to a different protein content, DNV-II containing about 600,000 daltons less protein, and to a different quaternary structure as indicated by the change in the density of DNV-II, in the presence of divalent cations, without any change in the density of DNV-I.

Centrifugation, Density Gradient↗

PubMed1998

A mathematical model for Neanderthal extinction.

A simple mathematical homogeneous model of competition is used to describe Neanderthal extinction in Europe. It considers two interacting species, Neanderthals and Early Modern Men, in the same ecological niche. Using paleontological data we claim that the parameter of similarity, between both species, fluctuates between 0.992 and 0.997. An extension of the model including migration (diffusion) is also discussed; nevertheless, extinction of Neanderthal seems unavoidable. Numerical analysis of travelling wave solutions (fronts) confirms the extinction. The wave-front-velocity is estimated from linear analysis and numerical simulations confirm this estimation. We conjecture a mathematical formulation for the principle of exclusion between competitive interacting species (Gause).

Animals↗

PubMedDate not supplied

Population extinction and recolonization in human demographic history.

For over 30 years, a debate has raged among anthropologists about the origins of anatomically modern humans. At first the debate centered on fossil evidence, but in the past 10-15 years population geneticists have entered the fray. One model, the multiregional evolution model, posits a gradual transition from Homo erectus to anatomically modern humans throughout the Old World. In contrast, the recent African origin model hypothesizes that anatomically modern humans arose from a small, isolated population in Africa, spread out of Africa, and replaced indigenous H. erectus populations in Eurasia and Australasia. A primary objection, from a population genetics perspective, to the multiregional model is that the genetic data suggest a small effective population size for humans. This effective size is on the order of 10,000. Effective population size has a complex relationship with census size, but it has been argued that, assuming that effective size is roughly equal to the number of breeding individuals in human populations under standard demographic conditions, 10,000 breeding individuals could not have occupied much of the Old World throughout the Pleistocene and remained a cohesive species via gene flow. However, this argument is not valid if one considers population extinction and recolonization, which might have played an important role in human history during the Pleistocene. With population extinction and recolonization, the inbreeding effective population size can be small and the census size extremely large. In this paper, I will show that under conditions of population extinction and recolonization, an effective population size of 10,000 suggested by genetic data is compatible with a large census size consistent with the multiregional model.

Animals↗

PubMed1981

Determination of some pyridinium aldoxime compounds by means of ion-pair reversed-phase high-performance liquid chromatography: application in biological material.

Two reversed-phase high-performance liquid chromatographic systems are presented for the separation and assay of the pyridinium aldoximes benzyl-P2A, HI-6 and obidoxime in aqueous solutions and biological samples. The systems involve a 5-micrometer C18 silica gel stationary phase. The eluent consists of methanol, acetic acid buffer (pH 4.80), a counter ion (per-chlorate or n-octanesulphonate) and a surfactant. The compounds were detected spectrophotometrically at 304 nm. In the concentration range used, linear plots of concentration versus extinction were obtained, both in blood and in water. Detection limits plots of concentration versus extinction were obtained, both in blood and in water. Detection limits, even in blood are satisfactory (0.5-1 microM). Evidence of presented that, at least for HI-6, the addition of counter ions to the system does not lead to the formation of ion pairs to be retained by partition, but rather to a mechanism based on adsorption chromatography.

2,2'-Dipyridyl↗

PubMed1998

Santa Rosalia revisited: why are there so many species of bacteria?

The diversity of bacteria in the world is very poorly known. Usually less than one percent of the bacteria from natural communities can be grown in the laboratory. This has caused us to underestimate bacterial diversity and biased our view of bacterial communities. The tools are now available to estimate the number of bacterial species in a community and to estimate the difference between communities. Using what data are available, I have estimated that thirty grams of forest soil contains over half a million species. The species difference between related communities suggests that the number of species of bacteria may be more than a thousand million. I suppose that the explanation for such a large number of bacterial species is simply that speciation in bacteria is easy and extinction difficult, giving a rate of speciation higher than the rate of extinction, leading to an ever increasing number of species over time. The idea that speciation is easy is justified from the results of recent experimental work in bacterial evolution.

Bacteria↗

PubMed2005

Neural crest origins of the neck and shoulder.

The neck and shoulder region of vertebrates has undergone a complex evolutionary history. To identify its underlying mechanisms we map the destinations of embryonic neural crest and mesodermal stem cells using Cre-recombinase-mediated transgenesis. The single-cell resolution of this genetic labelling reveals cryptic cell boundaries traversing the seemingly homogeneous skeleton of the neck and shoulders. Within this assembly of bones and muscles we discern a precise code of connectivity that mesenchymal stem cells of both neural crest and mesodermal origin obey as they form muscle scaffolds. The neural crest anchors the head onto the anterior lining of the shoulder girdle, while a Hox-gene-controlled mesoderm links trunk muscles to the posterior neck and shoulder skeleton. The skeleton that we identify as neural crest-derived is specifically affected in human Klippel-Feil syndrome, Sprengel's deformity and Arnold-Chiari I/II malformation, providing insights into their likely aetiology. We identify genes involved in the cellular modularity of the neck and shoulder skeleton and propose a new method for determining skeletal homologies that is based on muscle attachments. This has allowed us to trace the whereabouts of the cleithrum, the major shoulder bone of extinct land vertebrate ancestors, which seems to survive as the scapular spine in living mammals.

Amphibians↗

PubMed2003

Dispersal rates affect species composition in metacommunities of Sarracenia purpurea inquilines.

Dispersal among local communities can have a variety of effects on species composition and diversity at local and regional scales. Local conditions (e.g., resource and predator densities) can have independent effects, as well as interact with dispersal, to alter these patterns. Based on metacommunity models, we predicted that local diversity would show a unimodal relationship with dispersal frequency. We manipulated dispersal frequencies, resource levels, and the presence of predators (mosquito larvae) among communities found in the water-filled leaves of the pitcher plant Sarracenia purpurea. Diversity and abundance of species of the middle trophic level, protozoa and rotifers, were measured. Increased dispersal frequencies significantly increased regional species richness and protozoan abundance while decreasing the variance among local communities. Dispersal frequency interacted with predation at the local community scale to produce patterns of diversity consistent with the model. When predators were absent, we found a unimodal relationship between dispersal frequency and diversity, and when predators were present, there was a flat relationship. Intermediate dispersal frequencies maintained some species in the inquiline communities by offsetting extinction rates. Local community composition and the degree of connectivity between communities are both important for understanding species diversity patterns at local and regional scales.

Animals↗

PubMed1986

A three-zone model of soft-tissue damage by a CO2 laser.

CO2 laser damage to soft tissue may be divided into three zones--an outer layer of carbonised material, a zone of vacuolation where cavities have been formed by the explosive conversion of water to steam and a coagulated zone which has been formed at temperatures below 100 degrees C. A model is proposed which predicts the maximum (i.e. dynamic equilibrium) depths of each of these layers. The maximum effective thickness of the vacuolated zone is shown to depend upon the absorption coefficient of the tissue for CO2 laser radiation, but not on the incident irradiance. The thickness of the carbonised zone is shown to decrease with increasing irradiance, and the depth of the sub-boiling coagulated zone also decreases with increasing irradiance, but depends to some extent on the penetration of laser radiation through the soft tissue. Redistribution of heat within these zones after extinction of the laser radiation is considered, as is the effect of pulsed laser radiation. The predictions of the model could be tested by suitable experiments.

Carbon Dioxide↗