The Population Genetics of Evolutionary Rescue in Diploids: X Chromosomal versus Autosomal Rescue

Most population genetic theory assumes that populations adapt to an environmental change without a change in population size. However, environmental changes might be so severe that populations decline in size and, without adaptation, become extinct. This “evolutionary rescue” scenario differs from traditional models of adaptation in that rescue involves a race between adaptation and extinction. While most previous work has usually focused on models of evolutionary rescue in haploids, here we consider diploids. In many species, diploidy introduces a novel feature into adaptation: adaptive evolution might occur either on sex chromosomes or on autosomes. Previous studies of nonrescue adaptation revealed that the relative rates of adaptation on the X chromosome versus autosomes depend on the dominance of beneficial mutations, reflecting differences in effective population size and the efficacy of selection. Here, we extend these results to evolutionary rescue and find that, given equal-sized chromosomes, there is greater parameter space in which the X is more likely to contribute to adaptation than the autosomes relative to standard nonrescue models. We also discuss how subtle effects of dominance can increase the chance of evolutionary rescue in diploids when absolute heterozygote fitness is close to 1. These effects do not arise in standard nonrescue models.R00GM114714R01AI139154University of Rocheste

Population Extinction and the Genetics of Adaptation

Theories of adaptation typically ignore the effect of environmental change on population size. But some environmental challenges—challenges to which populations must adapt—may depress absolute fitness below 1, causing populations to decline. Under this scenario, adaptation is a race; beneficial alleles that adapt a population to the new environment must sweep to high frequency before the population becomes extinct. We derive simple, though approximate, solutions to the probability of successful adaptation (population survival) when adaptation involves new mutations, the standing genetic variation, or a mixture of the two. Our results show that adaptation to such environmental challenges can be difficult when relying on new mutations at one or a few loci, and populations will often decline to extinction

The Population Genetics of Evolutionary Rescue

Evolutionary rescue occurs when a population that is threatened with extinction by an environmental change adapts to the change sufficiently rapidly to survive. Here we extend the mathematical theory of evolutionary rescue. In particular, we model evolutionary rescue to a sudden environmental change when adaptation involves evolution at a single locus. We consider adaptation using either new mutations or alleles from the standing genetic variation that begin rare. We obtain several results: i) the total probability of evolutionary rescue from either new mutation or standing variation; ii) the conditions under which rescue is more likely to involve a new mutation versus an allele from the standing genetic variation; iii) a mathematical description of the U-shaped curve of total population size through time, conditional on rescue; and iv) the time until the average population size begins to rebound as well as the minimal expected population size experienced by a rescued population. Our analysis requires taking into account a subtle population-genetic effect (familiar from the theory of genetic hitchhiking) that involves “oversampling” of those lucky alleles that ultimately sweep to high frequency. Our results are relevant to conservation biology, experimental microbial evolution, and medicine (e.g., the dynamics of antibiotic resistance)

Sea Louse Infection of Juvenile Sockeye Salmon in Relation to Marine Salmon Farms on Canada's West Coast

BACKGROUND: Pathogens are growing threats to wildlife. The rapid growth of marine salmon farms over the past two decades has increased host abundance for pathogenic sea lice in coastal waters, and wild juvenile salmon swimming past farms are frequently infected with lice. Here we report the first investigation of the potential role of salmon farms in transmitting sea lice to juvenile sockeye salmon (Oncorhynchus nerka). METHODOLOGY/PRINCIPAL FINDINGS: We used genetic analyses to determine the origin of sockeye from Canada's two most important salmon rivers, the Fraser and Skeena; Fraser sockeye migrate through a region with salmon farms, and Skeena sockeye do not. We compared lice levels between Fraser and Skeena juvenile sockeye, and within the salmon farm region we compared lice levels on wild fish either before or after migration past farms. We matched the latter data on wild juveniles with sea lice data concurrently gathered on farms. Fraser River sockeye migrating through a region with salmon farms hosted an order of magnitude more sea lice than Skeena River populations, where there are no farms. Lice abundances on juvenile sockeye in the salmon farm region were substantially higher downstream of farms than upstream of farms for the two common species of lice: Caligus clemensi and Lepeophtheirus salmonis, and changes in their proportions between two years matched changes on the fish farms. Mixed-effects models show that position relative to salmon farms best explained C. clemensi abundance on sockeye, while migration year combined with position relative to salmon farms and temperature was one of two top models to explain L. salmonis abundance. CONCLUSIONS/SIGNIFICANCE: This is the first study to demonstrate a potential role of salmon farms in sea lice transmission to juvenile sockeye salmon during their critical early marine migration. Moreover, it demonstrates a major migration corridor past farms for sockeye that originated in the Fraser River, a complex of populations that are the subject of conservation concern

Evolutionary biology for the 21st century

New theoretical and conceptual frameworks are required for evolutionary biology to capitalize on the wealth of data now becoming available from the study of genomes, phenotypes, and organisms - including humans - in their natural environments.Molecular and Cellular BiologyOrganismic and Evolutionary Biolog

Young people today: news media, policy and youth justice

The new sociology of childhood sees children as competent social agents with important contributions to make. And yet the phase of childhood is fraught with tensions and contradictions. Public policies are required, not only to protect children, but also to control them and regulate their behaviour. For children and young people in the UK, youth justice has become increasingly punitive. At the same time, social policies have focused more on children's inclusion and participation. In this interplay of conflict and contradictions, the role the media play is critical in contributing to the moral panic about childhood and youth. In this article, we consider media representations of “antisocial” children and young people and how this belies a moral response to the nature of contemporary childhood. We conclude by considering how a rights-based approach might help redress the moralised politics of childhood representations in the media

Possibility of a White Dwarf as the Accreting Compact Star in CI Cam (= XTE J0421+560)

We present results from ASCA observations of the binary CI Cam both in quiescence and in outburst in order to identify its central accreting object. The quiescence spectrum of CI Cam consists of soft and hard components which are separated clearly at aound 2-3keV. A large equivalent width of an iron Ka emission line prefers an optically thin thermal plasma emission model to a non-thermal power-law model for the hard component, which favors a white dwarf as the accreting object, since the optically thin thermal hard X-ray emission is a common characteristic among cataclysmic variables (binaries including an accreting white dwarf). The outburst spectrum, on the other hand, is composed of a hard component represented by a multi-temperature optically thin thermal plasma emission and of an independent soft X-ray component that appears below 1 keV intermittently on a decaying light curve of the hard component. The spectrum of the soft component is represented well by a blackbody with the temperature of 0.07-0.12keV overlaid with several K-edges associated with highly ionized oxygen. This, together with the luminosity as high as ~1E38 erg/s is similar to a super-soft source (SSS). The outburst in the hard X-ray band followed by the appearance of the soft blackbody component reminds us of recent observations of novae in outburst. We thus assume the outburst of CI Cam is that of a nova, and obtain the distance to CI Cam to be 5-17kpc by means of the relation between the optical decay time and the absolute magnitude. This agrees well with a recent estimate of the distance of 5-9kpc in the optical band. All of these results from the outburst data prefer a white dwarf for the central object of CI Cam.Comment: 20 pages, 5 figures, to appear in the Astrophysical Journal v601, n2, February 1, 2004 issu

Supersymmetry without R-parity : Constraints from Leptonic Phenomenology

R-parity conservation is an {\it ad hoc} assumption in the most popular version of the supersymmetric standard model. Most studies of models which do allow for R-parity violation have been restricted to various limiting scenarios. The single-VEV parametrization used in this paper provides a workable framework to analyze phenomenology of the most general theory of SUSY without R-parity. We perform a comprehensive study of leptonic phenomenology at tree-level. Experimental constraints on various processes are studied individually and then combined to yield regions of admissible parameter space. In particular, we show that large R-parity violating bilinear couplings are not ruled out, especially for large $\tan\beta$.Comment: 56 pages Revtex with figures incorporated; typos (including transcription typo in Table II) and minor corrections; proof-read version, to appear in Phys. Rev.

Alternative lengthening of telomeres, ATRX loss and H3â K27M mutations in histologically defined pilocytic astrocytoma with anaplasia

Anaplasia may be identified in a subset of tumors with a presumed pilocytic astrocytoma (PA) component or piloid features, which may be associated with aggressive behavior, but the biologic basis of this change remains unclear. Fiftyâ seven resections from 36 patients (23 M, 13 F, mean age 32 years, range 3â 75) were included. A clinical diagnosis of NF1 was present in 8 (22%). Alternative lengthening of telomeres (ALT) was assessed by telomereâ specific FISH and/or CISH. A combination of immunohistochemistry, DNA sequencing and FISH were used to study BRAF, ATRX, CDKN2A/p16, mutant IDH1 p.R132H and H3â K27M proteins. ALT was present in 25 (69%) cases and ATRX loss in 20 (57%), mostly in the expected association of ALT+/ATRXâ (20/24, 83%) or ALTâ /ATRX+ (11/11, 100%). BRAF duplication was present in 8 (of 26) (31%). H3â K27M was present in 5 of 32 (16%) cases, all with concurrent ATRX loss and ALT. ALT was also present in 9 (of 11) cases in the benign PA precursor, 7 of which also had ATRX loss in both the precursor and the anaplastic tumor. In a single pediatric case, ALT and ATRX loss developed in the anaplastic component only, and in another adult case, ALT was present in the PAâ A component only, but ATRX was not tested. Features associated with worse prognosis included subtotal resection, adult vs. pediatric, presence of a PA precursor preceding a diagnosis of anaplasia, necrosis, presence of ALT and ATRX expression loss. ALT and ATRX loss, as well as alterations involving the MAPK pathway, are frequent in PA with anaplasia at the time of development of anaplasia or in their precursors. Additionally, a small subset of PA with anaplasia have H3â K27M mutations. These findings further support the concept that PA with anaplasia is a neoplasm with heterogeneous genetic features and alterations typical of both PA and diffuse gliomas.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/147190/1/bpa12646_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/147190/2/bpa12646.pd

First Principles Modeling of Nonlinear Incidence Rates in Seasonal Epidemics

In this paper we used a general stochastic processes framework to derive from first principles the incidence rate function that characterizes epidemic models. We investigate a particular case, the Liu-Hethcote-van den Driessche's (LHD) incidence rate function, which results from modeling the number of successful transmission encounters as a pure birth process. This derivation also takes into account heterogeneity in the population with regard to the per individual transmission probability. We adjusted a deterministic SIRS model with both the classical and the LHD incidence rate functions to time series of the number of children infected with syncytial respiratory virus in Banjul, Gambia and Turku, Finland. We also adjusted a deterministic SEIR model with both incidence rate functions to the famous measles data sets from the UK cities of London and Birmingham. Two lines of evidence supported our conclusion that the model with the LHD incidence rate may very well be a better description of the seasonal epidemic processes studied here. First, our model was repeatedly selected as best according to two different information criteria and two different likelihood formulations. The second line of evidence is qualitative in nature: contrary to what the SIRS model with classical incidence rate predicts, the solution of the deterministic SIRS model with LHD incidence rate will reach either the disease free equilibrium or the endemic equilibrium depending on the initial conditions. These findings along with computer intensive simulations of the models' Poincaré map with environmental stochasticity contributed to attain a clear separation of the roles of the environmental forcing and the mechanics of the disease transmission in shaping seasonal epidemics dynamics