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This paper concentrates on the general birth–death processes with two different types of catastrophes. The Laplace transform of transition probability function for birth–death processes with two-type catastrophes is successfully expressed with the Laplace transform of transition probability function of the birth–death processes without catastrophe. The first effective catastrophe occurrence time is considered. The Laplace transform of its probability density function, expectation and variance are obtained. [ABSTRACT FROM AUTHOR]

In this paper it is shown, that if a possibly inhomogeneous Markov chain with continuous time and finite state space is weakly ergodic and all the entries of its intensity matrix are locally integrable, then, using available results from the perturbation theory, its time-dependent probability characteristics can be approximately obtained from another Markov chain, having piecewise constant intensities and the same state space. The approximation error (the taxicab distance between the state probability distributions) is provided. It is shown how the Cauchy operator and the state probability distribution for an arbitrary initial condition can be calculated. The findings are illustrated with the numerical examples. [ABSTRACT FROM AUTHOR]

• We propose a temporal network model considering the stochastic phase transition of vertices. • Theoretical analysis is derived based on the continuous Markov chain method and confirmed by simulations. • Application in fitting the real network is discussed. Complex networks have played an important role in describing real complex systems since the end of the last century. Recently, research on real-world data sets reports intermittent interaction among social individuals. In this paper, we pay attention to this typical phenomenon of intermittent interaction by considering the state transition of network vertices between online and hidden based on the birth and death process. By continuous-time Markov theory, we show that both the number of each vertex's online neighbors and the online network size are stable and follow the homogeneous probability distribution in a similar form, inducing similar statistics as well. In addition, all propositions are verified via simulations. Moreover, we also present the degree distributions based on small-world and scale-free networks and find some regular patterns by simulations. The application in fitting real networks is discussed. [ABSTRACT FROM AUTHOR]

We consider a non-standard class of Markovian time: varying infinite capacity queues with possibly heterogeneous servers and impatience. We assume that during service time, a customer may switch to the faster server (with no delay), when such a server becomes available and no other customers are waiting. As a result, customers in the queue may become impatient and leave it. Under this setting and with certain restrictions on the intensity functions, the quantity of interest, the total number of customers in the system, is the level-dependent birth-and-death process (BPD). In this paper, for the first time in the literature, explicit upper bounds for the distance between two probability distributions of this BDP are obtained. Using the obtained ergodicity bounds in combination with the sensitivity bounds, we assess the stability of BDP under perturbations. Truncation bounds are also given, which allow for numerical solutions with guaranteed truncation errors. Finally, we provide numerical results to support the findings. [ABSTRACT FROM AUTHOR]

We construct a bio-inspired nanomachine network via the quorum sensing (QS) mechanism and analyze that nanonetwork from the perspective of global synchronization time and channel capacity. We propose a realistic (stochastic) approach using birth-death-process-based bacterial growth model and compare it to a conventional ideal (deterministic) approach using exponentially-increased bacterial growth model. For the comparative study, we first define a diffusion-based molecular communication channel between bacterial density and autoinducer (AI) concentration as an approximated Gaussian process, and then analyze the presented QS behavior model numerically as well as theoretically. Increases in the bacterial density augment the diffused AI concentration. When the AI concentration satisfies a specified threshold indicating gene expression, almost all bacteria in that colony represent a collective QS behavior such as biofilm formation. Compared to the ideal approach that is simple but not feasible in real life given the limited resources (e.g., food), the realistic approach is complex but better at representing real and probabilistic QS nature, less sensitive at gene expression, and so more suitable for global synchronization analysis. Via simulation, we evaluate the proposed model in terms of AI concentration versus bacterial density, synchronization time, and information sensing capacity, and demonstrate its superiority over the traditional model. [ABSTRACT FROM AUTHOR]

Decision trees are flexible models that are well suited for many statistical regression problems. In the Bayesian framework for regression trees, Markov Chain Monte Carlo (MCMC) search algorithms are required to generate samples of tree models according to their posterior probabilities. The critical component of such MCMC algorithms is to construct "good" Metropolis-Hastings steps to update the tree topology. Such algorithms frequently suffer from poor mixing and local mode stickiness; therefore, the algorithms are slow to converge. Hitherto, authors have primarily used discrete-time birth/death mechanisms for Bayesian (sums of) regression tree models to explore the tree-model space. These algorithms are efficient, in terms of computation and convergence, only if the rejection rate is low which is not always the case. We overcome this issue by developing a novel search algorithm which is based on a continuous-time birth-death Markov process. The search algorithm explores the tree-model space by jumping between parameter spaces corresponding to different tree structures. The jumps occur in continuous time corresponding to the birth-death events which are modeled as independent Poisson processes. In the proposed algorithm, the moves between models are always accepted which can dramatically improve the convergence and mixing properties of the search algorithm. We provide theoretical support of the algorithm for Bayesian regression tree models and demonstrate its performance in a simulated example. [ABSTRACT FROM AUTHOR]

Seed dispersals deal with complex systems through which the data collected using advanced seed tracking facilities pose challenges to conventional approaches, such as empirical and deterministic models. The use of stochastic models in current seed dispersal studies is encouraged. This review describes three existing stochastic models: the birth–death process (BDP), a 2 dimensional ( 2 D ) symmetric random walks and a 2 D intermittent walks. The three models possess Markovian property, which make them flexible for studying natural phenomena. Only a few of applications in ecology are found in seed dispersals. The review illustrates how the models are to be used in seed dispersals context. Using the nonlinear BDP, we formulate the individual-based models for two competing plant species while the cover time model is formulated by the symmetric and intermittent random walks. We also show that these three stochastic models can be formulated using the Gillespie algorithm. The full cover time obtained by the symmetric random walks can approximate the Gumbel distribution pattern as the other searching strategies do. We suggest that the applications of these models in seed dispersals may lead to understanding of many complex systems, such as the seed removal experiments and behaviour of foraging agents, among others. [ABSTRACT FROM AUTHOR]

Discrete-time birth-death processes may or may not have certain properties known as asymptotic aperiodicity and the strong ratio limit property. In all cases known to us a suitably normalized process having one property also possesses the other, suggesting equivalence of the two properties for a normalized process. We show that equivalence may be translated into a property involving Christoffel functions for a type of orthogonal polynomials known as random walk polynomials. The prevalence of this property – and thus the equivalence of asymptotic aperiodicity and the strong ratio limit property for a normalized birth-death process – is proven under mild regularity conditions. [ABSTRACT FROM AUTHOR]

In this paper, a mechanism called proximity inheritance is introduced in the birth–death process of a networked population involving the Prisoner's Dilemma game. Different from the traditional birth–death process, in the proposed model, players are distributed in a spatial space and offspring is distributed in the neighbourhood of its parents. That is, offspring inherits not only the strategy but also the proximity of its parents. In this coevolutionary game model, a cooperative neighbourhood gives more neighbouring cooperative offspring and a defective neighbourhood gives more neighbouring defective offspring, leading to positive feedback among cooperative interactions. It is shown that with the help of proximity inheritance, natural selection will favour cooperation over defection under various conditions, even in the presence of mutation. Furthermore, the coevolutionary dynamics could lead to self-organized substantial network clustering, which promotes an assortment of cooperative interactions. This study provides a new insight into the evolutionary mechanism of cooperation in the absence of social attributions such as reputation and punishment. [ABSTRACT FROM AUTHOR]

Planning a powerful server imposes an enormous cost for providing ideal performance. Given that a server responding for web requests is more likely to consume RAM memory than other resources, it is desirable to provide an appropriate RAM capacity for optimal performance of server in congested situations. This can be done through RAM usage modeling and its performance evaluation. In the literature, modeling of RAM usage is not provided with mathematical modeling. We propose an approach to model RAM usage of such a server, based on birth-death process in this article. The model can be used to figure out an operation research problem of finding minimum RAM capacity covering intended constraints elicited from birth-death queuing system. We show how optimal RAM capacity can be obtained using our approach with an illustrative example. [ABSTRACT FROM AUTHOR]

Insects rely on chemical information to locate food, choose mates, and detect potential predators. It has been hypothesized that adaptive changes in the olfactory system facilitated the diversification of numerous insect lineages. For instance, evolutionary changes of Odorant Receptor (OR) genes often occur in parallel with modifications in life history strategies. Corbiculate bees display a diverse array of behaviors that are controlled through olfaction, including varying degrees of social organization, and manifold associations with floral resources. Here we investigated the molecular mechanisms driving the evolution of the OR gene family in corbiculate bees in comparison to other chemosensory gene families. Our results indicate that the genomic organization of the OR gene family has remained highly conserved for ~80 Myr, despite exhibiting major changes in repertoire size among bee lineages. Moreover, the evolution of OR genes appears to be drivenmostly by lineage-specific gene duplications in few genomic regions that harbor large numbers of OR genes. A selection analysis revealed that OR genes evolve under positive selection, with the strongest signals detected in recently duplicated copies. Our results indicate that chromosomal translocations had a minimal impact on OR evolution, and instead local molecular mechanisms appear to be main drivers of OR repertoire size. Our results provide empirical support to the longstanding hypothesis that positive selection shaped the diversification of the OR gene family. Together, our results shed new light on the molecular mechanisms underlying the evolution of olfaction in insects. [ABSTRACT FROM AUTHOR]

We consider an extended birth–death–immigration process defined on a lattice formed by the integers of d semiaxes joined at the origin. When the process reaches the origin, then it may jump toward any semiaxis with the same rate. The dynamics on each ray evolves according to a one-dimensional linear birth–death process with immigration. We investigate the transient and asymptotic behavior of the process via its probability generating function. The stationary distribution, when existing, is a zero-modified negative binomial distribution. We also study a diffusive approximation of the process, which involves a diffusion process with linear drift and infinitesimal variance on each ray. It possesses a gamma-type transient density admitting a stationary limit. As a byproduct of our study, we obtain a closed form of the number of permutations with a fixed number of components, and a new series form of the polylogarithm function expressed in terms of the Gauss hypergeometric function. [ABSTRACT FROM AUTHOR]

Constructing a multi-dimensional prior on the times of divergence (the node ages) of species in a phylogeny is not a trivial task, in particular, if the prior density is the result of combining different sources of information such as a speciation process with fossil calibration densities. Yang & Rannala (2006 Mol. Biol. Evol. 23, 212-226. (doi:10.1093/molbev/msj024)) laid out the general approach to combine the birth-death process with arbitrary fossil-based densities to construct a prior on divergence times. They achieved this by calculating the density of node ages without calibrations conditioned on the ages of the calibrated nodes. Here, I show that the conditional density obtained by Yang & Rannala is misspecified. The misspecified density can sometimes be quite strange-looking and can lead to unintentionally informative priors on node ages without fossil calibrations. I derive the correct density and provide a few illustrative examples. Calculation of the density involves a sum over a large set of labelled histories, and so obtaining the density in a computer program seems hard at the moment. A general algorithm that may provide a way forward is given. This article is part of the themed issue 'Dating species divergences using rocks and clocks'. [ABSTRACT FROM AUTHOR]

The timing of perceptual decisions depends on both deterministic and stochastic factors, as the gradual accumulation of sensory evidence (deterministic) is contaminated by sensory and/or internal noise (stochastic). When human observers view multistable visual displays, successive episodes of stochastic accumulation culminate in repeated reversals of visual appearance. Treating reversal timing as a "first-passage time" problem, we ask how the observed timing densities constrain the underlying stochastic accumulation. Importantly, mean reversal times (i.e., deterministic factors) differ enormously between displays/observers/stimulation levels, whereas the variance and skewness of reversal times (i.e., stochastic factors) keep characteristic proportions of the mean. What sort of stochastic process could reproduce this highly consistent "scaling property?" Here we show that the collective activity of a finite population of bistable units (i.e., a generalized Ehrenfest process) quantitatively reproduces all aspects of the scaling property of multistable phenomena, in contrast to other processes under consideration (Poisson, Wiener, or Ornstein-Uhlenbeck process). The postulated units express the spontaneous dynamics of attractor assemblies transitioning between distinct activity states. Plausible candidates are cortical columns, or clusters of columns, as they are preferentially connected and spontaneously explore a restricted repertoire of activity states. Our findings suggests that perceptual representations are granular, probabilistic, and operate far from equilibrium, thereby offering a suitable substrate for statistical inference. [ABSTRACT FROM AUTHOR]

Background: Dosage balance has been described as an important process for the retention of duplicate genes after whole genome duplication events. However, dosage balance is only a temporary mechanism for duplicate gene retention, as it ceases to function following the stochastic loss of interacting partners, as dosage balance itself is lost with this event. With the prolonged period of retention, on the other hand, there is the potential for the accumulation of substitutions which upon release from dosage balance constraints, can lead to either subsequent neo-functionalization or sub-functionalization. Mechanistic models developed to date for duplicate gene retention treat these processes independently, but do not describe dosage balance as a transition state to eventual functional change. Results: Here a model for these processes (dosage plus neofunctionalization and dosage plus subfunctionalization) has been built within an existing framework. Because of the computational complexity of these models, a simpler modeling framework that captures the same information is also proposed. This model is integrated into a phylogenetic birth-death model, expanding the range of available models. Conclusions: Including further levels of biological reality in methods for gene tree/species tree reconciliation should not only increase the accuracy of estimates of the timing and evolutionary history of genes but can also offer insight into how genes and genomes evolve. These new models add to the tool box for characterizing mechanisms of duplicate gene retention probabilistically. [ABSTRACT FROM AUTHOR]

We consider sequences of polynomials that are defined by a three-terms recurrence relation and orthogonal with respect to a positive measure on the nonnegative axis. By a famous result of Karlin and McGregor such sequences are instrumental in the analysis of birth–death processes. Inspired by problems and results in this stochastic setting we present necessary and sufficient conditions in terms of the parameters in the recurrence relation for the smallest or second smallest point in the support of the orthogonalizing measure to be larger than zero, and for the support to be discrete with no finite limit point. [ABSTRACT FROM AUTHOR]

We study, for a given process $\mathcal{X}$, the conditions under which ν-similarity is provided, relations between similarity and ν-similarity of processes, and we analyze (doubly) limiting conditional distributions. We present sufficient conditions for the existence of at least one ν-similar process to a given one. Moreover, recursive formulas for birth and death rates of ν-similar processes are formulated. We apply differential equations and uniqueness of solutions to such equations to derive the main results of the paper. Finally, an example illustrates the applications of our results. [ABSTRACT FROM AUTHOR]

We prove that there exists a unique quasi-stationary distribution for the minimal birth–death process with exit boundary. A spectral representation for the quasi-stationary distribution is also obtained. [ABSTRACT FROM AUTHOR]

Background: Bayesian relaxed-clock dating has significantly influenced our understanding of the timeline of biotic evolution. This approach requires the use of priors on the branching process, yet little is known about their impact on divergence time estimates. We investigated the effect of branching priors using the iconic cycads. We conducted phylogenetic estimations for 237 cycad species using three genes and two calibration strategies incorporating up to six fossil constraints to (i) test the impact of two different branching process priors on age estimates, (ii) assess which branching prior better fits the data, (iii) investigate branching prior impacts on diversification analyses, and (iv) provide insights into the diversification history of cycads. Results: Using Bayes factors, we compared divergence time estimates and the inferred dynamics of diversification when using Yule versus birth-death priors. Bayes factors were calculated with marginal likelihood estimated with stepping-stone sampling. We found striking differences in age estimates and diversification dynamics depending on prior choice. Dating with the Yule prior suggested that extant cycad genera diversified in the Paleogene and with two diversification rate shifts. In contrast, dating with the birth-death prior yielded Neogene diversifications, and four rate shifts, one for each of the four richest genera. Nonetheless, dating with the two priors provided similar age estimates for the divergence of cycads from Ginkgo (Carboniferous) and their crown age (Permian). Of these, Bayes factors clearly supported the birth-death prior. Conclusions: These results suggest the choice of the branching process prior can have a drastic influence on our understanding of evolutionary radiations. Therefore, all dating analyses must involve a model selection process using Bayes factors to select between a Yule or birth-death prior, in particular on ancient clades with a potential pattern of high extinction. We also provide new insights into the history of cycad diversification because we found (i) periods of extinction along the long branches of the genera consistent with fossil data, and (ii) high diversification rates within the Miocene genus radiations. [ABSTRACT FROM AUTHOR]

Background: Bayesian relaxed-clock dating has significantly influenced our understanding of the timeline of biotic evolution. This approach requires the use of priors on the branching process, yet little is known about their impact on divergence time estimates. We investigated the effect of branching priors using the iconic cycads. We conducted phylogenetic estimations for 237 cycad species using three genes and two calibration strategies incorporating up to six fossil constraints to (i) test the impact of two different branching process priors on age estimates, (ii) assess which branching prior better fits the data, (iii) investigate branching prior impacts on diversification analyses, and (iv) provide insights into the diversification history of cycads. Results: Using Bayes factors, we compared divergence time estimates and the inferred dynamics of diversification when using Yule versus birth-death priors. Bayes factors were calculated with marginal likelihood estimated with stepping-stone sampling. We found striking differences in age estimates and diversification dynamics depending on prior choice. Dating with the Yule prior suggested that extant cycad genera diversified in the Paleogene and with two diversification rate shifts. In contrast, dating with the birth-death prior yielded Neogene diversifications, and four rate shifts, one for each of the four richest genera. Nonetheless, dating with the two priors provided similar age estimates for the divergence of cycads from Ginkgo (Carboniferous) and their crown age (Permian). Of these, Bayes factors clearly supported the birth-death prior. Conclusions: These results suggest the choice of the branching process prior can have a drastic influence on our understanding of evolutionary radiations. Therefore, all dating analyses must involve a model selection process using Bayes factors to select between a Yule or birth-death prior, in particular on ancient clades with a potential pattern of high extinction. We also provide new insights into the history of cycad diversification because we found (i) periods of extinction along the long branches of the genera consistent with fossil data, and (ii) high diversification rates within the Miocene genus radiations. [ABSTRACT FROM AUTHOR]

Objective: Copy number variation is now recognized as one of the major sources of genetic variation among individuals in natural populations of any species. However, the relevance of these unexpected observations goes beyond diagnosing high diversity. Results: Here, it is argued that the molecular rates of copy number variation, mainly the deletion rate upon variation, determine the evolutionary road of the genome regarding size. Genetic drift will govern this process only if the effective population size is lower than the inverse of the deletion rate. Otherwise, natural selection will do. [ABSTRACT FROM AUTHOR]

Abstract: We propose an infinitesimal dispersion index for Markov counting processes. We show that, under standard moment existence conditions, a process is infinitesimally (over-)equi-dispersed if, and only if, it is simple (compound), i.e. it increases in jumps of one (or more) unit(s), even though infinitesimally equi-dispersed processes might be under-, equi- or over-dispersed using previously studied indices. Compound processes arise, for example, when introducing continuous-time white noise to the rates of simple processes resulting in Lévy-driven SDEs. We construct multivariate infinitesimally over-dispersed compartment models and queuing networks, suitable for applications where moment constraints inherent to simple processes do not hold. [Copyright &y& Elsevier]

The study of paleopolyploidies requires the comparison of multiple whole genome sequences. If the branches of a phylogeny on which a whole-genome duplication (WGD) occurred could be identified before genome sequencing, taxa could be selected that provided a better assessment of that genome duplication. Here, we describe a likelihood model in which the number of chromosomes in a genome evolves according to a Markov process with one rate of chromosome duplication and loss that is proportional to the number of chromosomes in the genome and another stochastic rate at which every chromosome in the genome could duplicate in a single event. We compare the maximum likelihoods of a model in which the genome duplication rate varies to one in which it is fixed at zero using the Akaike information criterion, to determine if a model with WGDs is a good fit for the data. Once it has been determined that the data does fit the WGD model, we infer the phylogenetic position of paleopolyploidies by calculating the posterior probability that a WGD occurred on each branch of the taxon tree. Here, we apply this model to a molluscan tree represented by 124 taxa and infer three putative WGD events. In the Gastropoda, we identify a single branch within the Hypsogastropoda and one of two branches at the base of the Stylommatophora. We also identify one or two branches near the base of the Cephalopoda. [ABSTRACT FROM AUTHOR]

Quantitative traits have long been hypothesized to affect speciation and extinction rates. For example, smaller body size or increased specialization may be associated with increased rates of diversification. Here, I present a phylogenetic likelihood-based method (quantitative state speciation and extinction [QuaSSE]) that can be used to test such hypotheses using extant character distributions. This approach assumes that diversification follows a birth–death process where speciation and extinction rates may vary with one or more traits that evolve under a diffusion model. Speciation and extinction rates may be arbitrary functions of the character state, allowing much flexibility in testing models of trait-dependent diversification. I test the approach using simulated phylogenies and show that a known relationship between speciation and a quantitative character could be recovered in up to 80% of the cases on large trees (500 species). Consistent with other approaches, detecting shifts in diversification due to differences in extinction rates was harder than when due to differences in speciation rates. Finally, I demonstrate the application of QuaSSE to investigate the correlation between body size and diversification in primates, concluding that clade-specific differences in diversification may be more important than size-dependent diversification in shaping the patterns of diversity within this group. [ABSTRACT FROM PUBLISHER]

Abstract: We establish some representations for the smallest and largest zeros of orthogonal polynomials in terms of the parameters in the three-terms recurrence relation. As a corollary we obtain representations for the endpoints of the true interval of orthogonality. Implications of these results for the decay parameter of a birth–death process (with killing) are displayed. [Copyright &y& Elsevier]

Time-calibrated molecular phylogenies provide a valuable window into the tempo and mode of species diversification, especially for the large number of groups that lack adequate fossil records. Molecular phylogenetic data frequently suggest an initial “explosive speciation” phase, leading to widespread speculation that ecological niche-filling processes might govern the dynamics of species diversification during evolutionary radiations. However, these patterns are difficult to reconcile with the fossil record. The fossil record strongly suggests that extinction rates have been high relative to speciation rates, but such elevated background extinction should erase the signal of early, rapid speciation from molecular phylogenies. For this reason, extinction rates in molecular phylogenies are frequently estimated as zero under the widely used birth–death model. Here, I construct a simple model that combines phylogenetically patterned extinction with pulsed turnover dynamics and constant diversity through time. Using approximate Bayesian methods, I show that heritable extinction can easily explain the phenomenon of explosive early diversification, even when net diversification rates are equal to zero. Several assumptions of the model are more consistent with both the fossil record and neontological data than the standard birth–death model and it may thus represent a viable alternative interpretation of phylogenetic diversification patterns. These results suggest that variation in the absolute rate of lineage turnover through time, in conjunction with phylogenetically nonrandom extinction, may underlie the apparent diversity-dependent speciation observed in molecular phylogenies. [ABSTRACT FROM PUBLISHER]

Species traits may influence rates of speciation and extinction, affecting both the patterns of diversification among lineages and the distribution of traits among species. Existing likelihood approaches for detecting differential diversification require complete phylogenies; that is, every extant species must be present in a well-resolved phylogeny. We developed 2 likelihood methods that can be used to infer the effect of a trait on speciation and extinction without complete phylogenetic information, generalizing the recent binary-state speciation and extinction method. Our approaches can be used where a phylogeny can be reasonably assumed to be a random sample of extant species or where all extant species are included but some are assigned only to terminal unresolved clades. We explored the effects of decreasing phylogenetic resolution on the ability of our approach to detect differential diversification within a Bayesian framework using simulated phylogenies. Differential diversification caused by an asymmetry in speciation rates was nearly as well detected with only 50% of extant species phylogenetically resolved as with complete phylogenetic knowledge. We demonstrate our unresolved clade method with an analysis of sexual dimorphism and diversification in shorebirds (Charadriiformes). Our methods allow for the direct estimation of the effect of a trait on speciation and extinction rates using incompletely resolved phylogenies. [ABSTRACT FROM PUBLISHER]

Many hormones are secreted in pulses. The pulsatile relationship between hormones regulates many biological processes. To understand endocrine system regulation, time series of hormone concentrations are collected. The goal is to characterize pulsatile patterns and associations between hormones. Currently each hormone on each subject is fitted univariately. This leads to estimates of the number of pulses and estimates of the amount of hormone secreted; however, when the signal-to-noise ratio is small, pulse detection and parameter estimation remains difficult with existing approaches. In this article, we present a bivariate deconvolution model of pulsatile hormone data focusing on incorporating pulsatile associations. Through simulation, we exhibit that using the underlying pulsatile association between two hormones improves the estimation of the number of pulses and the other parameters defining each hormone. We develop the one-to-one, driver–response case and show how birth–death Markov chain Monte Carlo can be used for estimation. We exhibit these features through a simulation study and apply the method to luteinizing and follicle stimulating hormones. [ABSTRACT FROM AUTHOR]

We describe a simple comparative method for determining whether rates of diversification are correlated with continuous traits in species-level phylogenies. This involves comparing traits of species with net speciation rate (number of nodes linking extant species with the root divided by the root to tip evolutionary distance), using a phylogenetically corrected correlation.We use simulations to examine the power of this test. We find that the approach has acceptable power to uncover relationships between speciation and a continuous trait and is robust to background random extinction; however, the power of the approach is reduced when the rate of trait evolution is decreased. The test has low power to relate diversification to traits when extinction rate is correlated with the trait. Clearly, there are inherent limitations in using only data on extant species to infer correlates of extinction; however, this approach is potentially a powerful tool in analyzing correlates of speciation. [ABSTRACT FROM AUTHOR]

The number of sensory receptor genes varies extensively among different mammalian species. This variation is believed to be caused partly by physiological requirements of animals and partly by genomic drift due to random duplication and deletion of genes. If the contribution of genomic drift is substantial, each species should contain a significant amount of copy number variation (CNV). We therefore investigated CNVs in sensory receptor genes among 270 healthy humans by using published CNV data. The results indicated that olfactory receptor (OR), taste receptor type 2, and vomeronasal receptor type 1 genes show a high level of intraspecific CNVs. In particular, >30% of the ≈800 OR gene loci in humans were polymorphic with respect to copy number, and two randomly chosen individuals showed a copy number difference of ≈11 in functional OR genes on average. There was no significant difference in the amount of CNVs between functional and non-functional OR genes. Because pseudogenes are expected to evolve in a neutral fashion, this observation suggests that functional OR genes also have evolved in a similar manner with respect to copy number change. In addition, we found that the evolutionary change of copy number of OR genes approximately follows the Gaussian process in probability theory, and the copy number divergence between populations has increased with evolutionary time. We therefore conclude that genomic drift plays an important role for generating intra- and interspecific CNVs of sensory receptor genes. Similar results were obtained when all annotated genes were analyzed. [ABSTRACT FROM AUTHOR]

Determining whether speciation and extinction rates depend on the state of a particular character has been of long-standing interest to evolutionary biologists. To assess the effect of a character on diversification rates using likelihood methods requires that we be able to calculate the probability that a group of extant species would have evolved as observed, given a particular model of the character's effect. Here we describe how to calculate this probability for a phylogenetic tree and a two-state (binary) character under a simple model of evolution (the "BiSSE" model, binary-state speciation and extinction). The model involves six parameters, specifying two speciation rates (rate when the lineage is in state 0; rate when in state 1), two extinction rates (when in state 0; when in state 1), and two rates of character state change (from 0 to 1, and from 1 to 0). Using these probability calculations, we can do maximum likelihood inference to estimate the model's parameters and perform hypothesis tests (e.g., is the rate of speciation elevated for one character state over the other?). We demonstrate the application of the method using simulated data with known parameter values. [ABSTRACT FROM AUTHOR]

The coarse-grained Monte Carlo (CGMC) algorithm was originally proposed in the series of works [M. A. Katsoulakis, A. J. Majda, and D. C. Vlachos, J. Comput. Phys., 186 (2003), pp. 250-278; M. A. Katsoulakis, A. J. Majda, and D. G. Vlachos, Proc. Nati. Acad. Sci. USA, 100 (2003), pp. 782-787; M. A. Katsoulakis and D. G. Vlachos, J. Chem. Phys., 119 (2003), pp. 9412-9427]. In this paper we further investigate the approximation properties of the coarse-graining procedure and provide both analytical and numerical evidence that the hierarchy of the coarse models is built in a systematic way that allows for error control in both transient and long-time simulations. We demonstrate that the numerical accuracy of the CGMC algorithm as an approximation of stochastic lattice spin flip dynamics is of order two in terms of the coarse-graining ratio and that the natural small parameter is the coarse-graining ratio over the range of particle/particle interactions. The error estimate is shown to hold in the weak convergence sense. We employ the derived analytical results to guide CGMC algorithms and demonstrate a CPU speed-up in demanding computational regimes that involve nucleation, phase transitions, and metastability. [ABSTRACT FROM AUTHOR]

In this paper, a model for the radiation treatment of cancer which includes the effects of the cell cycle is derived from first principles. A malignant cell population is divided into two compartments based on radiation sensitivities. The active compartment includes the four phases of the cell cycle, while the quiescent compartment consists of the G0 state. Analysis of this active-quiescent radiation model confirms the classical interpretation of the linear quadratic (LQ) model, which is that a larger α/β ratio corresponds to a fast cell cycle, while a smaller ratio corresponds to a slow cell cycle. Additionally, we find that a large α/β ratio indicates the existence of a significant quiescent phase. The active-quiescent model is extended as a nonlinear birth–death process in order to derive an explicit time dependent expression for the tumour control probability (TCP). This work extends the TCP formula from Zaider and Minerbo and it enables the TCP to be calculated for general time dependent treatment schedules. [ABSTRACT FROM AUTHOR]

In many chronic conditions, subjects alternate between an active and an inactive state, and sojourns into the active state may involve multiple lesions, infections, or other recurrences with different times of onset and resolution. We present a biologically interpretable model of such chronic recurrent conditions based on a queueing process. The model has a birth–death process describing recurrences and a semi-Markov process describing the alternation between active and inactive states, and can be fit to panel data that provide only a binary assessment of the active or inactive state at a series of discrete time points using a hidden Markov approach. We accommodate individual heterogeneity and covariates using a random effects model, and simulate the posterior distribution of unknowns using a Markov chain Monte Carlo algorithm. Application to a clinical trial of genital herpes shows how the method can characterize the biology of the disease and estimate treatment efficacy. [ABSTRACT FROM AUTHOR]

The current paper surveys and develops numerical methods for Markovian multitype branching processes in continuous time. Particular attention is paid to the calculation of means, variances, extinction probabilities, and marginal distributions in the presence of a Poisson stream of immigrant particles. The Poisson process assumption allows for temporally complex patterns of immigration and facilitates application of marked Poisson processes and Campbell's formulas. The methods and formulas derived are applied to four models: two population genetics models, a model for vaccination against an infectious disease in a community of households, and a model for the growth of resistant HIV virus in patients undergoing drug therapy. [ABSTRACT FROM AUTHOR]

Primula sect. Auricula is one of only a few endemics of the European high mountains with a comparatively large number of species. We explored the section's geographical origin, time of origin, and temporal course of diversification via parsimony, genetic distance, and lineages-through-time analyses based on the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA. The taxa analyzed included 52 individuals representing all 25 species of the section, representatives of seven other European, Asian, and/or North American sections of the genus, and two species of Douglasia. We present evidence that sect. Auricula likely originated from an Asian ancestor at the end of the Late Tertiary, followed by its primary diversification into an ‘eastern’ and ‘western’ lineage at the Plio-/Pleistocene boundary. Comparison with a constant rates null model of stochastic diversification-extinction (birth-death) demonstrates that diversification has proceeded nonrandomly through Quaternary times in both lineages. They display a pulse of speciation events occurring soon after their origin and relatively few such events occurring since. This pattern contrasts with the predictions of the Late Pleistocene origins hypothesis and implies unpredictability of the evolutionary response of sect. Auricula to the recurrent abiotic conditions of the Quaternary glacial-interglacial cycles. We conclude that it is not necessary to invoke an increase in extinction rate. Rather, the observed slowdown of interspecific (and intraspecific) diversification in sect. Auricula toward the present likely results from a decrease in diversification rate due to ecological and/or geographical space-filling processes. [ABSTRACT FROM AUTHOR]

We consider sequences of orthogonal polynomials and pursue the question of how (partial) knowledge of the orthogonalizing measure for the associated polynomials can lead to information about the orthogonalizing measure for the original polynomials. In particular, we relate the supports of the two measures, and their moments. As an application, we analyze the relation between two decay rates connected with a birth–death process. [Copyright &y& Elsevier]

We consider the logistic growth model and analyze its relevant properties, such as the limits, the monotony, the concavity, the inflection point, the maximum specific growth rate, the lag time, and the threshold crossing time problem. We also perform a comparison with other growth models, such as the Gompertz, Korf, and modified Korf models. Moreover, we focus on some stochastic counterparts of the logistic model. First, we study a time-inhomogeneous linear birth-death process whose conditional mean satisfies an equation of the same form of the logistic one. We also find a sufficient and necessary condition in order to have a logistic mean even in the presence of an absorbing endpoint. Then, we obtain and analyze similar properties for a simple birth process, too. Then, we investigate useful strategies to obtain two time-homogeneous diffusion processes as the limit of discrete processes governed by stochastic difference equations that approximate the logistic one. We also discuss an interpretation of such processes as diffusion in a suitable potential. In addition, we study also a diffusion process whose conditional mean is a logistic curve. In more detail, for the considered processes we study the conditional moments, certain indices of dispersion, the first-passage-time problem, and some comparisons among the processes. [ABSTRACT FROM AUTHOR]

The model of a two-dimensional birth-death process with possible catastrophes is studied. The upper bounds on the rate of convergence in some weighted norms and the corresponding perturbation bounds are obtained. In addition, we consider the detailed description of two examples with 1-periodic intensities and various types of death (service) rates. The bounds on the rate of convergence and the behavior of the corresponding mathematical expectations are obtained for each example. [ABSTRACT FROM AUTHOR]

Abstract: We correct representations for the endpoints of the true interval of orthogonality of a sequence of orthogonal polynomials that were stated by us in the Journal of Computational and Applied Mathematics 233 (2009) 847–851. [Copyright &y& Elsevier]