Population dynamics, demographic stochasticity, and the evolution of cooperation

A basic evolutionary problem posed by the Iterated Prisoner’s Dilemma game is to understand when the paradigmatic cooperative strategy Tit-for-Tat can invade a population of pure defectors. Deterministically, this is impossible. We consider the role of demographic stochasticity by embedding the Iterated Prisoner’s Dilemma into a population dynamic framework. Tit-for-Tat can invade a population of defectors when their dynamics exhibit short episodes of high population densities with subsequent crashes and long low density periods with strong genetic drift. Such dynamics tend to have reddened power spectra and temporal distributions of population size that are asymmetric and skewed toward low densities. The results indicate that ecological dynamics are important for evolutionary shifts between adaptive peaks.

Prevalence of serious eye disease and visual impairment in a north London population: population based, cross sectional study

Objective: To estimate the magnitude of serious eye disorders and of visual impairment in a defined elderly population of a typical metropolitan area in England, and to assess the frequency they were in touch with, or known to, the eye care services.

Digging for dead genes: an analysis of the characteristics of the pseudogene population in the Caenorhabditis elegans genome

Pseudogenes are non-functioning copies of genes in genomic DNA, which may either result from reverse transcription from an mRNA transcript (processed pseudogenes) or from gene duplication and subsequent disablement (non-processed pseudogenes). As pseudogenes are apparently ‘dead’, they usually have a variety of obvious disablements (e.g., insertions, deletions, frameshifts and truncations) relative to their functioning homologs. We have derived an initial estimate of the size, distribution and characteristics of the pseudogene population in the Caenorhabditis elegans genome, performing a survey in ‘molecular archaeology’. Corresponding to the 18 576 annotated proteins in the worm (i.e., in Wormpep18), we have found an estimated total of 2168 pseudogenes, about one for every eight genes. Few of these appear to be processed. Details of our pseudogene assignments are available from http://bioinfo.mbb.yale.edu/genome/worm/pseudogene. The population of pseudogenes differs significantly from that of genes in a number of respects: (i) pseudogenes are distributed unevenly across the genome relative to genes, with a disproportionate number on chromosome IV; (ii) the density of pseudogenes is higher on the arms of the chromosomes; (iii) the amino acid composition of pseudogenes is midway between that of genes and (translations of) random intergenic DNA, with enrichment of Phe, Ile, Leu and Lys, and depletion of Asp, Ala, Glu and Gly relative to the worm proteome; and (iv) the most common protein folds and families differ somewhat between genes and pseudogenes—whereas the most common fold found in the worm proteome is the immunoglobulin fold and the most common ‘pseudofold’ is the C-type lectin. In addition, the size of a gene family bears little overall relationship to the size of its corresponding pseudogene complement, indicating a highly dynamic genome. There are in fact a number of families associated with large populations of pseudogenes. For example, one family of seven-transmembrane receptors (represented by gene B0334.7) has one pseudogene for every four genes, and another uncharacterized family (represented by gene B0403.1) is approximately two-thirds pseudogenic. Furthermore, over a hundred apparent pseudogenic fragments do not have any obvious homologs in the worm.

Changes in the prevalence of chronic disability in the United States black and nonblack population above age 65 from 1982 to 1999

Survey evidence through the early 1990s generally suggests a reduction in disability in the elderly population of the United States. Because the evidence is not fully consistent, several authors have speculated about whether disability declines will continue. This paper reports results from the 1999 National Long-Term Care Survey on disability trends from 1982 through 1999. It is found that disability continued to decline in the 1994 to 1999 period, and that the decline was greater in the 1990s than in the 1980s. The disability decline from 1982 to 1989 was 0.26% per year, from 1989 to 1994 it was 0.38% per year, and from 1994 to 1999 it was 0.56% per year. In addition, disability declined by a greater percentage for blacks than for nonblacks over the 1989 to 1999 period.

Genetic drift and within-host metapopulation dynamics of HIV-1 infection

Most HIV replication occurs in solid lymphoid tissue, which has prominent architecture at the histological level, which separates groups of productively infected CD4+ cells. Nevertheless, current population models of HIV assume panmixis within lymphoid tissue. We present a simple “metapopulation” model of HIV replication, where the population of infected cells is comprised of a large number of small populations, each of which is established by a few founder viruses and undergoes turnover. To test this model, we analyzed viral genetic variation of infected cell subpopulations within the spleen and demonstrated the action of founder effects as well as significant variation in the extent of genetic differentiation between subpopulations among patients. The combination of founder effects and subpopulation turnover can result in an effective population size much lower than the actual population size and may contribute to the importance of genetic drift in HIV evolution despite a large number of infected cells.

Sex ratio adjustment in relation to paternal attractiveness in a wild bird population.

When the relative fitness of sons and daughters differs, sex-allocation theory predicts that it would be adaptive for individuals to adjust their investment in different sexes of offspring. Sex ratio adjustment by females in response to the sexual attractiveness of their mate would be an example of this. In vertebrates the existence of this form of sex ratio adjustment is controversial and may be confounded with sex-biased mortality, particularly in sexually size-dimorphic species. Here we use PCR amplification of a conserved W-chromosome-linked gene to show that the sex ratio within broods of a natural population of sexually size-monomorphic collared flycatchers Ficedula albicollis is related to the size of their father's forehead patch, a heritable secondary sexual character implicated in female choice. Experimental manipulations of paternal investment, which influence the size of his character in future breeding attempts, result in corresponding changes in the sex ratio of offspring born to males in those breeding attempts. In contrast, manipulations of maternal investment have no effect on future sex ratios, and there is no relationship between variables predicting the reproductive value of the brood and nestling sex ratio. Analysis of recruitment of offspring reveals similar patterns of sex ratio bias. The results suggest that female collared flycatchers be able to adjust the sex ratio of eggs ovulated in response to the phenotype of their mate. This finding is most consistent with "genetic quality" models of sexual selection.

Modeling and optimization of populations subject to time-dependent mutation.

It has become clear that many organisms possess the ability to regulate their mutation rate in response to environmental conditions. So the question of finding an optimal mutation rate must be replaced by that of finding an optimal mutation schedule. We show that this task cannot be accomplished with standard population-dynamic models. We then develop a "hybrid" model for populations experiencing time-dependent mutation that treats population growth as deterministic but the time of first appearance of new variants as stochastic. We show that the hybrid model agrees well with a Monte Carlo simulation. From this model, we derive a deterministic approximation, a "threshold" model, that is similar to standard population dynamic models but differs in the initial rate of generation of new mutants. We use these techniques to model antibody affinity maturation by somatic hypermutation. We had previously shown that the optimal mutation schedule for the deterministic threshold model is phasic, with periods of mutation between intervals of mutation-free growth. To establish the validity of this schedule, we now show that the phasic schedule that optimizes the deterministic threshold model significantly improves upon the best constant-rate schedule for the hybrid and Monte Carlo models.

Heritable, population-wide damage to cells as the driving force of neoplastic transformation.

Prolonged incubation of NIH 3T3 cells under the growth constraint of confluence results in the death of some cells in a manner suggestive of apoptosis. Successive rounds of prolonged incubation at confluence of the surviving cells produce increasing neoplastic transformation in the form of increments in saturation density and transformed focus formation. Cells from the postconfluent cultures are given a recovery period of various lengths to remove the direct inhibitory effect of confluence before their growth properties are studied. It is found that with each round of confluence the exponential growth rate of the cells at low densities gets lower and the size of isolated colonies of the same cells shows a similar progressive reduction. The decreased growth rate of cells from the third round of confluence persists for > 60 generations of growth at low density. The proportion of colonies containing giant cells is much higher after a 2-day recovery from confluence than after a 7-day recovery. Retardation of growth at low density and increased saturation density appear to be two sides of the same coin: both occur in the entire population of cells and precede the formation of transformed foci. We propose that the slowdown in growth and the formation of giant cells result from heritable damage to the cells, which in turn drives their transformation. Similar results have been reported for the survivors of x-irradiation and of treatment with chemical carcinogens and are associated with the aging process in animals. We suggest that these changes result from free radical damage to membrane lipids with particular damage to lysosomes. Proteases and nucleases would then be released to progressively modify the growth behavior and genetic stability of the cells toward autonomous proliferation.

Pathways to quiescence: SHARDS view on the star formation histories of massive quiescent galaxies at 1.0 < z < 1.5

We present star formation histories (SFHs) for a sample of 104 massive (stellar mass M > 10^10 M_⊙) quiescent galaxies (MQGs) at z = 1.0–1.5 from the analysis of spectrophotometric data from the Survey for High-z Absorption Red and Dead Sources (SHARDS) and HST/WFC3 G102 and G141 surveys of the GOODS-North field, jointly with broad-band observations from ultraviolet (UV) to far-infrared (far-IR). The sample is constructed on the basis of rest-frame UVJ colours and specific star formation rates (sSFRs = SFR/Mass). The spectral energy distributions (SEDs) of each galaxy are compared to models assuming a delayed exponentially declining SFH. A Monte Carlo algorithm characterizes the degeneracies, which we are able to break taking advantage of the SHARDS data resolution, by measuring indices such as MgUV and D4000. The population of MQGs shows a duality in their properties. The sample is dominated (85 per cent) by galaxies with young mass-weighted ages, t_M t_M < 2 Gyr, short star formation time-scales, 〈τ〉 ∼ 60–200 Myr, and masses log(M/M_⊙) ∼ 10.5. There is an older population (15 per cent) with t_M t_M = 2–4 Gyr, longer star formation time-scales, 〈τ〉∼ 400 Myr, and larger masses, log(M/M_⊙) ∼ 10.7. The SFHs of our MQGs are consistent with the slope and the location of the main sequence of star-forming galaxies at z > 1.0, when our galaxies were 0.5–1.0 Gyr old. According to these SFHs, all the MQGs experienced a luminous infrared galaxy phase that lasts for ∼500 Myr, and half of them an ultraluminous infrared galaxy phase for ∼100 Myr. We find that the MQG population is almost assembled at z ∼ 1, and continues evolving passively with few additions to the population.

Census of breeding birds and population trends of the Dupont’s lark Chersophilus duponti in eastern Spain

We present the results of a breeding census of Dupont’s Lark carried out in the Autonomous Community of Valencia in 2011 using the mapping method and an analysis of the recent trend for this population. The population was estimated at 44-47 males, located in five habitat patches of the Rincón de Ademuz, in zones where the species had been detected previously. Density in these patches fits within values expected according to the relation between patch size and density found in the populations of the nearby provinces. Comparison to previous studies reveals that population of Valencia has suffered an annual decline rate of around 10% on average, thus the implementation of a conservation plan is required to ensure the survival of the species in the study area.

A highly resistive layer within the crust of X-ray pulsars limits their spin periods

The lack of isolated X-ray pulsars with spin periods longer than 12 s raises the question of where the population of evolved high-magnetic-field neutron stars has gone. Unlike canonical radiopulsars, X-ray pulsars are not subject to physical limits to the emission mechanism nor observational biases against the detection of sources with longer periods. Here we show that a highly resistive layer in the innermost part of the crust of neutron stars naturally limits the spin period to a maximum value of about 10–20 s. This highly resistive layer is expected if the inner crust is amorphous and heterogeneous in nuclear charge, possibly owing to the existence of a nuclear ‘pasta’ phase. Our findings suggest that the maximum period of isolated X-ray pulsars may be the first observational evidence for an amorphous inner crust, whose properties can be further constrained by future X-ray timing missions combined with more detailed models.

Indicators of obesity and the educational attainment of the Czech female population

The aim of this paper was to evaluate the relationship between selected indicators of obesity and the highest completed level of education in the adult female population of the Czech republic. As basic indicators of obesity, these following parameters were selected and measured via the bioimpedance method on the device InBody 720: BMI, WHR (waist-to-hip ratio), % body fat, % skeletal muscle mass, fitness score. The educational attainment of the tested women was inquired by a questionnaire. Based on the responses, we subsequently divided our sample into four categories according to the level of education: primary education, secondary education-apprenticeship, secondary education-graduate diploma, and university. The research was realized within the project CZ.1.07/2.3.00/20.0044. The measurements on the device InBody 720 and the accompanying survey were conducted between 2011-2013 in different regions of the Czech Republic. The sample consisted of 754 women divided into 3 age groups (18-39, 40-59, 60+ years). Based on the results (p<0.05), we can say that average values of the indicators obesity (BMI: 22.76, 24.88, 26.49 kg/m2, WHR: 0.85, 0.88, 0.90 and % body fat: 25.76, 30.23, 34.62%) increase with the increasing age of examined women. The average values of the fitness score (75.53, 73.86, 70.04 points) and % skeletal muscle mass (40.78, 38.15, 33.95%) decrease with increasing age. With regard to the educational attainment, women with secondary education-apprenticeship achieved the worst results. In contrast, the values in university educated women were the best in most indicators of obesity.

Use of an Inverse Method for Time Series to Estimate the Dynamics of and Management Strategies for the Box Jellyfish Carybdea marsupialis

Frequently, population ecology of marine organisms uses a descriptive approach in which their sizes and densities are plotted over time. This approach has limited usefulness for design strategies in management or modelling different scenarios. Population projection matrix models are among the most widely used tools in ecology. Unfortunately, for the majority of pelagic marine organisms, it is difficult to mark individuals and follow them over time to determine their vital rates and built a population projection matrix model. Nevertheless, it is possible to get time-series data to calculate size structure and densities of each size, in order to determine the matrix parameters. This approach is known as a “demographic inverse problem” and it is based on quadratic programming methods, but it has rarely been used on aquatic organisms. We used unpublished field data of a population of cubomedusae Carybdea marsupialis to construct a population projection matrix model and compare two different management strategies to lower population to values before year 2008 when there was no significant interaction with bathers. Those strategies were by direct removal of medusae and by reducing prey. Our results showed that removal of jellyfish from all size classes was more effective than removing only juveniles or adults. When reducing prey, the highest efficiency to lower the C. marsupialis population occurred when prey depletion affected prey of all medusae sizes. Our model fit well with the field data and may serve to design an efficient management strategy or build hypothetical scenarios such as removal of individuals or reducing prey. TThis This sdfsdshis method is applicable to other marine or terrestrial species, for which density and population structure over time are available.

Tracing the Origins of Athlete Development Models in Sport: a Citation Path Analysis

Reviews of the sport psychology literature have identified a number of models of athlete development in sport (Alfermann & Stambulova, 2007; Durand-Bush &Salmela, 2001). However, minimal research has investigated the origins of knowledge from which each model was developed. The purpose of this study was to systematically examine the influential texts responsible for providing the basis of athlete development models in sport. A citation path analysis of the sport psychology literature was used to generate a knowledge development path of seven athlete development models in sport. The analysis identified influential texts and authors in the conceptualization of athlete development. The popula-tion of 229 texts (articles, books, book chapters) was selected in two phases. Phase1 texts were articles citing seven articles depicting models of athlete development(n  75). Phase 2 included texts cited three or more times by Phase 1 articles (n  154). The analysis revealed how the scholarship of Benjamin Bloom (1985) has been integrated into the field of sport psychology, and how two articles appearing in 1993 and 2003 helped shape present conceptualizations of athlete development

West Indies and British Guiana : Return to an address of the Honourable The House of Commons dated 29 May 1845, for "copies of the last census of the population taken in each of the British West India Islands and in British Guiana, specifying their respective dates; together with any information subsequently received ... relative to the number of the emancipated Negroes who have become freeholders, the extent of land purchased by them, and the sums of money paid or payable for such purchases." Ordered, by the House of Commons, to be printed, 30 June 1845 /

"(Mr. Barkly)."