A hierarchical Bayesian model for calibrating estimates of species divergence times

In Bayesian divergence time estimation methods, incorporating calibrating information from the fossil record is commonly done by assigning prior densities to ancestral nodes in the tree. Calibration prior densities are typically parametric distributions offset by minimum age estimates provided by the fossil record. Specification of the parameters of calibration densities requires the user to quantify his or her prior knowledge of the age of the ancestral node relative to the age of its calibrating fossil. The values of these parameters can, potentially, result in biased estimates of node ages if they lead to overly informative prior distributions. Accordingly, determining parameter values that lead to adequate prior densities is not straightforward. In this study, I present a hierarchical Bayesian model for calibrating divergence time analyses with multiple fossil age constraints. This approach applies a Dirichlet process prior as a hyperprior on the parameters of calibration prior densities. Specifically, this model assumes that the rate parameters of exponential prior distributions on calibrated nodes are distributed according to a Dirichlet process, whereby the rate parameters are clustered into distinct parameter categories. Both simulated and biological data are analyzed to evaluate the performance of the Dirichlet process hyperprior. Compared with fixed exponential prior densities, the hierarchical Bayesian approach results in more accurate and precise estimates of internal node ages. When this hyperprior is applied using Markov chain Monte Carlo methods, the ages of calibrated nodes are sampled from mixtures of exponential distributions and uncertainty in the values of calibration density parameters is taken into account.     

A model of microbial contamination of a water reservoir

A three year record of daily fecal coliform counts in a Massachusetts water reservoir has the appearance of an irregular time series punctuated by outbursts of varying duration. The pattern is described in terms of a probabilistic model where the fluctuations in the ‘regular’ and ‘explosive’ regimes are governed by two sets of probabilities. It has been assumed that the random oscillations has a lognormal distribution, and that once an explosion threshold has been exceeded the increments or decrements in the population size have fixed probability distributions. The threshold for triggering an outburst was estimated by examining the randomness of the autocorrelation function of the record after it is filtered to eliminate peaks of progressively increasing magnitude. Once the threshold has been identified, the mean and standard deviation of the underlying lognormal distribution could be estimated directly from remains found in the record after all the peaks were removed. The probabilities of an increment and decrement during the outbursts and their relative magnitudes could also be estimated using simple formulas. These estimated parameter values were then used to generate realistic records with known threshold levels, which were subsequently used to assess the procedure’s feasibility and sensitivity.     

To what extent do new fossil discoveries change our understanding of clade evolution? A cautionary tale from burying beetles (Coleoptera: Nicrophorus)

Divergence time estimates derived from phylogenies are crucial to infer historical biogeography and diversification dynamics. Yet, the impact of fossil record incompleteness on macroevolutionary reconstructions remains equivocal. Here, we investigate to what extent gaps in the fossil record can impinge downstream evolutionary inferences in the beetle family Silphidae. Recent discoveries have pushed back the fossil record of this group from the Eocene into the Jurassic. We estimated the divergence times of the family using both its currently understood fossil record and the fossil record known prior to these recent discoveries. All fossil calibrations were informed with different parametric distributions to investigate the weight of priors on posterior age estimates. Based on time‐calibrated trees, we assessed the impact of fossil calibrations on the inference of ancestral ranges and diversification rate dynamics in the genus Nicrophorus. Depending upon the selected sets of fossil constraints, the age discrepancies had a major impact on the macroevolutionary inferences: the biogeographic extrapolations relative to paleogeography are markedly contrasting, and the calculated rates at which species form or go extinct (and when they varied) are strikingly different. We show that soft prior distributions do not necessarily alleviate such shortcomings therefore preventing the inference of reliable macroevolutionary patterns in groups presenting a taphonomic bias in their fossil record.     

Niche expansion and temperature sensitivity of tropical African montane forests

Aim Climate and land‐use change will have a dramatic impact on future ecosystems through alterations to species ranges and community composition. When forming conservation strategies, correlative species distribution models are often created to assess risks for individual species. These models are based on the assumption of climatic equilibrium, such that the modern range is representative of the full range of conditions under which species could thrive. However, the palaeo‐ecological record illustrates examples of disequilibrium in species today, and recent studies suggest that many species could occur in much broader climatic settings than previously thought. Montane ecosystems are thought to be at disproportionate risk due to temperature sensitivity and restricted geographical ranges. However, in the Afrotropics the palaeo‐ecological record shows that montane forest taxa expanded into the lowlands numerous times, suggesting a possible tolerance to warm temperatures. Location Africa. Methods We integrate palaeo‐ecological and palaeo‐climatic data in order to compare climate conditions in which species are currently found with those in the past. We use species distribution models to construct potential modern ranges for Afromontane species based on modern distributions and distributions in the palaeo‐ecological record in order to evaluate the equilibrium of species ranges. Results We show that many Afromontane trees have occupied warmer climates in the past, which suggests that the current low‐elevation boundaries are not set by climate. Interestingly, the species with the largest disequilibrium between palaeo‐ and modern distributions are those whose modern distributions show the least temperature sensitivity. Mapping of species potential ranges based on modern and palaeo‐ distributions clearly shows that suitable climate conditions exist today in the lowlands for less temperature‐sensitive species. Main conclusions These results imply that the current range of these forest trees does not necessarily inform risk from climatic change, and that human land use may be the major pressure for many species in the future.     

On Concomitants of Order Statistics from Morgenstern Family

In the present paper the distribution theory of concomitants of order statistics from the Morgenstern family of distribution is investigated. An application of the results in providing some quick estimates of the parameters in the Gumbel's bivariate exponential distribution is also discussed.     

金黄角头小蜂及寄主新纪录(膜翅目:小蜂科)

金黄角头小蜂Dirhinus auratus Ashmead(小蜂科:角头小蜂亚科)在中国大陆首次纪录,研究标本均由家蝇蛹放于室外诱集后饲养获得;家蝇蛹为金黄角头小蜂的寄主新记录.本文提供了金黄角头金小蜂形态描述、分布及形态特征图.研究标本保存在中国科学院动物研究所动物标本馆及安徽师范大学标本馆.     

The gender-specific apolipoprotein E genotype influence on the distribution of plasma lipids and apolipoproteins in the population of Rochester, Minnesota. II. Regression relationships with concomitants.

The influence of the apolipoprotein E (Apo E) polymorphism and gender on the regression relationships between each of nine plasma lipid and apolipoprotein traits (total cholesterol; ln triglycerides; high-density-lipoprotein cholesterol; apolipoproteins AI, AII, B, and CII; ln CIII; and ln E) and four concomitants (age, weight, waist-to-hip ratio, and smoking) was studied in 507 unrelated individuals representative of the adult population of Rochester, MN. Analyses are presented separately for females and males. Each lipid and apolipoprotein trait exhibited at least one Apo E genotype-specific regression relationship with the concomitants investigated in this study. In most cases the heterogeneity of regression was associated with differences between the epsilon 32 and epsilon 33 genotype. This study documents that the influence of Apo E genotype on average levels of plasma lipids and apolipoproteins varies among subdivisions of the population defined by age, body size, and smoking status.     

Search for the association of polymorphic markers for genes coding for antioxidant defense enzymes, with development of diabetic polyneuropathies in patients with type 1 diabetes mellitus

The allele and genotype frequency distributions of polymorphic markers of genes coding for antioxidant enzymes were compared for type 1 diabetes mellitus patients with or without diabetic polyneuropathy (DPN). The groups (total 180 patients) had nonoverlapping (polar) phenotypes. Group DPN+ included 86 patients with DPN and diabetic record no more than 5 years. Control group DPN- included patients without DPN and diabetic record of at least 10 years. Comparative analysis with Fisher's exact test revealed a significant difference in allele and genotype frequency distributions of the T(-262)C polymorphic marker of the CAT gene. Polymorphic markers C1167T of the CAT gene, Pro/Leu of the GPX1 gene, 0/+ of the GSTT1 gene, and 0/+ of the GSTM1 gene showed no significant difference in allele or genotype frequency distribution. On this evidence, these markers were not associated with DPN in the sample examined.     

试论种子顽拗性的复合数量性状特征

文章简要概述了从顽拗型种子到顽拗性种子这样一个对顽拗性种子认识提高的过程,在综述了前人关于顽拗性种子数量性状特征论述的基础上,把种子顽拗性的数量性状特征划分为种间、种内和个体发育三个层面,提出种子顽拗性是一种复合性状,其核心至少包括脱水耐性、低温耐性和贮藏耐性三方面的内容,其伴随性状包括种子尺度、千粒重、初始含水量、休眠特性、分类地位、地理分布和保护性物质含量等多方面的内容,而且这些核心内容和伴随性状的每一个方面都具有渐变的、过渡的、数量型的特征,从而阐明种子顽拗性是一种复合数量性状.种子顽拗性的复合数量性状特征的提出及其三个层面的划分,有助于加深对种子顽拗性的认识,并用以指导我们在实践中解决种子顽拗性方面的具体问题.     

Proteaceae Leaf Fossils: Phylogeny,Diversity, Ecology and Austral Distributions

Foliar fossils of Proteaceae are reviewed, and useful specimens for interpreting evolution, and past and present distributions and environments are discussed. There are no definite Cretaceous occurrences. However, there is evidence of extant lineages dating from the Paleocene onwards, including tribe Persoonieae of subfamily Persoonioideae and each of the four tribes of subfamily Grevilleoideae. High diversity and abundance characterizes the Australian fossil record, including sclerophyllous and xeromorphic forms, but there is little evidence of the prominent extant subfamily Proteoideae. New Zealand had a much higher diversity of Proteaceae than at present, including Oligo-Miocene species of open vegetation. The South American leaf fossil record is not extensive. However, the fossil records of Embothrieae and Orites are consistent with the distributions of their extant relatives in South America and Australia being the result of vicariance. Overall, there is a need for more research on placing Proteaceae leaf fossils in a phylogenetic context.     

Genetics of increased lifespan in Drosophila

Natural selection in the laboratory has been used to produce populations of Drosophila with genetically increased lifespan. These populations have been used to determine the physiological basis of postponed ageing and its pleiotropic concomitants. It appears that many loci and a number of physiological alterations are involved in increased lifespan.     

A review of the fossil record of monocotyledons

The fossil record of monocotyledons is reviewed in order to determine the families actually represented by fossils and their stratigraphic ranges. In providing this information, attention is called to deficiencies and strengths in the record. Most notable is the uneven representation of the four subclasses of monocotyledons. Three distinct phases in the history of monocots can be delineated when the record and ranges of modern families are compared with paleotemperature data. First is a phase of initial radiation and diversification primarily restricted to the Cretaceous and represented by the appearance of a variety of monocotyledonous leaf forms. Second is a phase of modernization of the monocot flora resulting from further development of preexisting Cretaceous forms during favorable climatic conditions during the latest Cretaceous and Paleogene. The third phase is one marked by changes in distributions and expansion of other groups corresponding with climatic deteriorations of the late Paleogene. Some suggestions concerning the limitations of and potential for further research into the fossil record of monocots are presented.     

Multiple-source models for electron beams of a medical linear accelerator using BEAMDP computer code

AimThe aim of this work was to develop multiple-source models for electron beams of the NEPTUN 10PC medical linear accelerator using the BEAMDP computer code.BackgroundOne of the most accurate techniques of radiotherapy dose calculation is the Monte Carlo (MC) simulation of radiation transport, which requires detailed information of the beam in the form of a phase-space file. The computing time required to simulate the beam data and obtain phase-space files from a clinical accelerator is significant. Calculation of dose distributions using multiple-source models is an alternative method to phase-space data as direct input to the dose calculation system.Materials and methodsMonte Carlo simulation of accelerator head was done in which a record was kept of the particle phase-space regarding the details of the particle history. Multiple-source models were built from the phase-space files of Monte Carlo simulations. These simplified beam models were used to generate Monte Carlo dose calculations and to compare those calculations with phase-space data for electron beams.ResultsComparison of the measured and calculated dose distributions using the phase-space files and multiple-source models for three electron beam energies showed that the measured and calculated values match well each other throughout the curves.ConclusionIt was found that dose distributions calculated using both the multiple-source models and the phase-space data agree within 1.3%, demonstrating that the models can be used for dosimetry research purposes and dose calculations in radiotherapy.     

Sharks that pass in the night: using Geographical Information Systems to investigate competition in the Cretaceous Western Interior Seaway

One way the effects of both ecology and environment on species can be observed in the fossil record is as changes in geographical distribution and range size. The prevalence of competitive interactions and species replacements in the fossil record has long been investigated and many evolutionary perspectives, including those of Darwin, have emphasized the importance of competitive interactions that ultimately lead one species to replace another. However, evidence for such phenomena in the fossil record is not always manifest. Here we use new quantitative analytical techniques based on Geographical Information Systems and PaleoGIS tectonic reconstructions to consider this issue in greater detail. The abundant, well-preserved fossil marine vertebrates of the Late Cretaceous Western Interior Seaway of North America provide the component data for this study. Statistical analysis of distributional and range size changes in taxa confirms earlier ideas that the relative frequency of competitive replacement in the fossil record is limited to non-existent. It appears that typically, environmental gradients played the primary role in determining species distributions, with competitive interactions playing a more minor role.     

ASTHMA ALTERNATING WITH PSYCHIATRIC SYMPTOMATOLOGY

A group of cases and review of the literature is presented documenting the interesting clinical phenomenon of an inverse temporal relationship between asthmatic symptoms and clinical psychiatric symptoms in some patients. It is suggested that physicians treating asthmatic patients should be prepared to handle potential psychiatric complications that may be concomitants of the successful medical management of patients with asthma.     

Differences in saliva collection location and disparities in baseline and diurnal rhythms of alpha-amylase: A preliminary note of caution

Identified in the early 1980s as a surrogate marker of the sympathetic nervous system component of the stress response, there has been renewed interest in measuring salivary alpha-amylase (sAA) to test biosocial models of stress vulnerability. This brief report presents studies that document that oral fluids from the parotid and submandibular gland areas had higher sAA values than did whole saliva specimens, and sAA values in whole saliva were higher than levels measured in oral fluids from the sublingual gland area. sAA in oral fluids from the parotid and submandibular gland areas showed the highest and more pronounced diurnal variation than levels in whole saliva, and sAA in sublingual saliva showed the lowest and shallowest diurnal variation. When this source of inherent variability in sAA activity levels is not controlled for by collecting oral fluids consistently from specific gland areas, the detection of individual differences, associations between sAA and “behavioral” variables, and intra-individual change in sAA levels may be compromised. Awareness, and management, of this ubiquitous source of measurement error in sAA are essential to ensure the success of future research on the correlates and concomitants of sAA levels, stress-related reactivity and recovery, and diurnal variation.     

Differences in saliva collection location and disparities in baseline and diurnal rhythms of alpha-amylase: a preliminary note of caution

Identified in the early 1980s as a surrogate marker of the sympathetic nervous system component of the stress response, there has been renewed interest in measuring salivary alpha-amylase (sAA) to test biosocial models of stress vulnerability. This brief report presents studies that document that oral fluids from the parotid and submandibular gland areas had higher sAA values than did whole saliva specimens, and sAA values in whole saliva were higher than levels measured in oral fluids from the sublingual gland area. sAA in oral fluids from the parotid and submandibular gland areas showed the highest and more pronounced diurnal variation than levels in whole saliva, and sAA in sublingual saliva showed the lowest and shallowest diurnal variation. When this source of inherent variability in sAA activity levels is not controlled for by collecting oral fluids consistently from specific gland areas, the detection of individual differences, associations between sAA and “behavioral” variables, and intra-individual change in sAA levels may be compromised. Awareness, and management, of this ubiquitous source of measurement error in sAA are essential to ensure the success of future research on the correlates and concomitants of sAA levels, stress-related reactivity and recovery, and diurnal variation.     

Taxonomy of the genus Acymatopus Takagi (Diptera: Dolichopodidae)

Two new species of the genus Acymatopus from Japan and China are described. This is the first record of Acymatopus outside Japan. A key to all six valid species of the genus is given, and their distributions are mapped and discussed.     

Species abundance distributions over time

It has been known for 50 years that the time period over which data are collected affects the shape of empirical species abundance distributions. However, despite a recent resurgence of interest in characterizing and explaining these patterns the temporal component of species abundance distributions has been largely ignored. I argue that it is essential to take account of time, and not only because sampling duration can have a profound influence on the perceived shape of the distribution. Partitions of species abundance distributions based on temporal occurrence in the record will facilitate tests of both biological and neutral models and may lead to a better understanding of rarity. These temporal partitions also have interesting, but as yet barely explored, parallels with spatial ones such as the core-satellite division. Moreover, changes in abundance distributions across all three of Preston's temporal scales (sampling time, ecological time and evolutionary time) present rich opportunities for ecological research.     

Lymphokine-induced changes in macrophage transmembrane electrical potentials

Intracellular electrical potentials have been measured in nonactivated and immunologically-activated macrophages obtained from the peritoneal cavities of mice. Normal macrophage potentials were established and found to become significantly more electronegative after in vitro exposure for 10 minutes to a lymphokine-containing supernatant which induced macrophage activation. This approach may reflect very early concomitants of such activation and is also useful in the study of other immunologic systems.