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PubMed2000

Effects of natural selection on patterns of DNA sequence variation at the transferrin, somatolactin, and p53 genes within and among chinook salmon (Oncorhynchus tshawytscha) populations.

This paper describes DNA sequence variation within and among four populations of chinook salmon (Oncorhynchus tshawytscha) at the transferrin, somatolactin and p53 genes. Patterns of variation among salmon species at the transferrin gene have been hypothesized to be shaped by positive natural selection for new alleles because the rate of nonsynonymous substitution is significantly greater than the rate of synonymous substitution. The twin goals of this study were to determine if the history of selection among salmon species at the transferrin gene is also reflected in patterns of intraspecific variation in chinook salmon, and to look for evidence of local adaptation at the transferrin gene by comparing patterns of nonsynonymous and synonymous variation among chinook salmon populations. The analyses presented here show that unlike patterns of variation between species, there is no evidence of greater differentiation among chinook salmon populations at nonsynonymous compared to synonymous sites. There is also no evidence of a reduction of within-species variation due to the hitchhiking effect at the transferrin gene, although in some populations nonsynonymous and synonymous derived mutations are both at higher frequencies than expected under a simple neutral model. Population size weighted selection coefficients (4Ns) that are consistent with both the inter and intraspecific data range from approximately 10 to approximately 235, and imply that between 1 and 40% of new nonsynonymous mutations at the transferrin gene have been beneficial.

Alleles↗
PubMed2002

The contribution of haploids, diploids and clones to fine-scale population structure in the seaweed Cladophoropsis membranacea (Chlorophyta).

Local populations of Cladophoropsis membranacea exist as mats of coalesced thalli composed of free-living haploid and diploid plants including clonally reproduced plants of either phase. None of the phases are morphologically distinguishable. We used eight microsatellite loci to explore clonality and fine-scale patch structure in C. membranacea at six sites on the Canary Islands. Mats were always composites of many individuals; not single, large clones. Haploids outnumbered diploids at all sites (from 2:1 to 10:1). In both haploid and diploid plants, genetic diversity was high and there was no significant difference in allele frequencies. Significant heterozygote deficiencies were found in the diploid plants at five out of six sites and linkage disequilibrium was associated with the haploid phase at all sites. Short dispersal distances of gametes/spores and small effective population sizes associated with clonality probably contribute to inbreeding. Spatial autocorrelation analysis revealed that most clones were found within a radius of approximately 60 cm and rarely further than 5 m. Dominance of the haploid phase may reflect seasonal shifts in the relative frequencies of haploids and diploids, but may alternatively reflect superiority of locally adapted and competitively dominant, haploid clones; a strategy that is theoretically favoured in disturbed environments. Although sexual reproduction may be infrequent in C. membranacea, it is sufficient to maintain both life history phases and supports theoretical modelling studies that show that haploid-diploid life histories are an evolutionarily stable strategy.

Chlorophyta↗
PubMed2003

Cryptic species, cryptic endosymbionts, and geographical variation in chemical defences in the bryozoan Bugula neritina.

Molecular markers often offer the only means to discriminate between species and to elucidate the specificity of many community interactions, both of which are key to the understanding of ecological patterns. Western Atlantic populations of the bryozoan Bugula neritina vary in the palatability of their larvae to predators: individuals south of Cape Hatteras produce chemical deterrents to fish predators that are absent in more northern individuals. We use mitochondrial cytochrome oxidase c subunit I (COI) sequences to show that the differences in palatability between populations correlate with the geographical distributions of two cryptic species within B. neritina. Furthermore, these cryptic species differ in their associations with bacteria that may confer chemical resistance to predation. Small subunit rRNA primers specific to a subset of gamma-proteobacteria amplified only the bacterium Endobugula sertula from the southern cryptic species. Endobugula sertula produces a family of chemical compounds (bryostatins) that may deter predators of its animal host. In contrast, the same primers amplified an array of gamma-proteobacteria from the unprotected northern cryptic bryozoan species, but never E. sertula. In combination, these findings suggest that the geographical variation in palatability observed in the larvae of B. neritina is not the result of local adaptation of a single species to regions of differing predation pressure, but rather results from the comparison of cryptic species that differ in the presence or absence of a bacterium that may provide protection against predators. The ability to identify the cryptic Bugula species and their differing relationships with bacterial associates provides an example of the important role molecular techniques may play in addressing ecological questions.

Animals↗
PubMed2003

Hierarchical spatial structure of genetically variable nucleopolyhedroviruses infecting cyclic populations of western tent caterpillars.

The cyclic population dynamics of western tent caterpillars, Malacosoma californicum pluviale, are associated with epizootics of a nucleopolyhedrovirus, McplNPV. Given the dynamic fluctuations in host abundance and levels of viral infection, host resistance and virus virulence might be expected to change during different phases of the cycle. As a first step in determining if McplNPV virulence and population structure change with host density, we used restriction fragment length polymorphism (RFLP) analysis to examine the genetic diversity of McplNPV infecting western tent caterpillar populations at different spatial scales. Thirteen dominant genetic variants were identified in 39 virus isolates (individual larvae) collected from field populations during one year of low host density, and another distinct variant was discovered among nine additional isolates in two subsequent years of declining host density. The distribution of these genetic variants was not random and indicated that the McplNPV population was structured at several spatial levels. A high proportion of the variation could be explained by family grouping, which suggested that isolates collected within a family were more likely to be the same than isolates compared among populations. Additionally, virus variants from within populations (sites) were more likely to be the same than isolates collected from tent caterpillar populations on different islands. This may indicate that there is limited mixing of virus among tent caterpillar families and populations when host population density is low. Thus there is potential for the virus to become locally adapted to western tent caterpillar populations in different sites. However, no dominant genotype was observed at any site. Whether and how selection acts on the genetically diverse nucleopolyhedrovirus populations as host density changes will be investigated over the next cycle of tent caterpillar populations.

Animals↗
PubMed2003

The role of environment in shaping the genetic diversity of the subalpine mosquito, Aedes rusticus (Diptera, Culicidae).

The relative involvement of larval dietary tolerance to the leaf-litter toxic polyphenols in shaping population genetic structure of the subalpine mosquito Aedes rusticus was examined. This was compared with other parameters such as geographical range, type of vegetation surrounding the breeding site, and occurrence of annual larvicidal treatments. Population genetic structure was analysed at 10 presumed neutral polymorphic isoenzyme loci. Toxicological comparisons involved standard bioassays performed on larvae fed on toxic decomposed leaf litter. Significant overall genetic differentiation was observed among the 22 studied populations and within the five defined geographical groups. Analysis of molecular variance revealed an absence of relation between genetic and environmental parameters, genetic variance being essentially found within populations. This suggested that the larval dietary tolerance to the toxic leaf litter and the other studied parameters poorly influence population genetic structure. The local adaptation of subalpine mosquito populations to the surrounding vegetation thus appears as a labile trait. Such a dynamic adaptation is also suggested by the correlation between geographical and toxicological distances and the correlation between dietary tolerance to the leaf-litter toxic polyphenols and annual larvicidal treatments.

Aedes↗
PubMed2004

Adherence to the combination of sulphadoxine-pyrimethamine and artesunate in the Maheba refugee settlement, Zambia.

Artemisinin-based combination therapy (ACT) is one strategy recommended to increase cure rates in malaria and to contain resistance to Plasmodium falciparum. In the Maheba refugee settlement, children aged 5 years or younger with a confirmed diagnosis of uncomplicated falciparum malaria are treated with the combination of sulphadoxine-pyrimethamine (1 day) and artesunate (3 days). To measure treatment adherence, home visits were carried out the day after the last treatment dose. Patients who had any treatment dose left were considered certainly non-adherent. Other patients' classification was based on the answers to the questionnaire: patients whose caretakers stated the child had received the treatment regimen exactly as prescribed were considered probably adherent; all other patients were considered probably non-adherent. Reasons for non-adherence were assessed. We found 21.2% (95% CI [15.0-28.4]) of the patients to be certainly non-adherent, 39.4% (95% CI [31.6-47.6]) probably non-adherent, and 39.4% (95% CI [31.6-47.6]) probably adherent. Insufficient explanation by the dispenser was identified as an important reason for non-adherence. When considering the use of ACT, the issue of patient adherence remains challenging. However, it should not be used as an argument against the introduction of ACT. For these treatment regimens to remain efficacious on a long-term basis, specific and locally adapted strategies need to be implemented to ensure completion of the treatment.

Antimalarials↗
PubMed2001

Implementing guidelines about colorectal cancer: a national survey of target groups.

BACKGROUND: An Australia-wide postal survey was undertaken to determine surgeons' attitudes towards guidelines and their preferred strategies for dissemination and implementation of guidelines for the management of colorectal cancer, developed by the Australian Cancer Network (ACN) and the Clinical Oncological Society of Australia (COSA). This survey was conducted as a baseline before the release of the definitive guidelines. METHODS: All members of the Royal Australasian College of Surgeons (RACS) with a self-nominated special interest in colorectal surgery and members of the Colorectal Surgical Society of Australia (CSSA) were surveyed. RESULTS: A total of 195 of the 219 surgeons eligible for the study returned questionnaires (89% response rate). Most (86%) were aware that these guidelines were being developed. More than one-half had read at least one draft version. Almost half (44.6%; 95%CI: 37.6-51.9%) agreed that guidelines represented 'cookbook medicine' and one-third (33.3%; 95%CI: 26.9-40.5%) agreed that guidelines might increase the number of malpractice suits. Local adaptation of guidelines and 'academic detailing' were most favourably ranked to assure implementation. Further, 54.9% (95%CI: 47.6-61.9%) of respondents believed that a successful legal defence of a surgeon whose practice had been within the guidelines would encourage uptake. Surgeons operating outside teaching hospitals were more likely to endorse this view than others. CONCLUSIONS: These results demonstrate that an important target group for colorectal cancer guidelines, namely surgeons, appears receptive to clinical practice guidelines. These results could also permit interventions that target attitudinal barriers to implementing guidelines and subgroups of surgeons who have particular concerns. Expensive strategies for implementation ought to be subject to rigorous evaluation for their impact in modifying clinical practice.

Attitude of Health Personnel↗
PubMed2002

Evidence for positive selection and population structure at the human MAO-A gene.

We report the analysis of human nucleotide diversity at a genetic locus known to be involved in a behavioral phenotype, the monoamine oxidase A gene. Sequencing of five regions totaling 18.8 kb and spanning 90 kb of the monoamine oxidase A gene was carried out in 56 male individuals from seven different ethnogeographic groups. We uncovered 41 segregating sites, which formed 46 distinct haplotypes. A permutation test detected substantial population structure in these samples. Consistent with differentiation between populations, linkage disequilibrium is higher than expected under panmixia, with no evidence of a decay with distance. The extent of linkage disequilibrium is not typical of nuclear loci and suggests that the underlying population structure may have been accentuated by a selective sweep that fixed different haplotypes in different populations, or by local adaptation. In support of this suggestion, we find both a reduction in levels of diversity (as measured by a Hudson-Kreitman-Aguade test with the DMD44 locus) and an excess of high frequency-derived variants, as expected after a recent episode of positive selection.

Animals↗
PubMed2005

Interface connections of a transmembrane voltage sensor.

Voltage-sensitive ion channels open and close in response to changes in transmembrane (TM) potential caused by the motion of the S4 voltage sensors. These sensors are alpha-helices that include four or more positively charged amino acids, most commonly arginine. The so-called paddle model, based on the high-resolution structure of the KvAP K+ channel [Jiang, et al. (2003) Nature 423, 33-41], posits that the S4 sensors move within the membrane bilayer in response to TM voltage changes. Direct exposure of S4 sensors to lipid is contrary to the classical expectation that the dielectric contrast between the membrane hydrocarbon core and water presents an insurmountable energetic penalty to burial of electric charges. Nevertheless, recent experiments have shown that a helix with the sequence of KvAP S4 can be inserted across the endoplasmic reticulum membrane. To reconcile this result with the classical energetics argument, we have carried out a molecular dynamics simulation of an isolated TM S4 helix in a lipid bilayer. The simulation reveals a stabilizing hydrogen-bonded network of water and lipid phosphates around the arginines that reduces the effective thickness of the bilayer hydrocarbon core to approximately 10 A in the vicinity of the helix. It suggests that bilayer phospholipids can adapt locally to strongly perturbing protein elements, causing the phospholipids to become a structural extension of the protein.

Hydrogen Bonding↗
PubMed2003

Biocomplexity and fisheries sustainability.

A classic example of a sustainable fishery is that targeting sockeye salmon in Bristol Bay, Alaska, where record catches have occurred during the last 20 years. The stock complex is an amalgamation of several hundred discrete spawning populations. Structured within lake systems, individual populations display diverse life history characteristics and local adaptations to the variation in spawning and rearing habitats. This biocomplexity has enabled the aggregate of populations to sustain its productivity despite major changes in climatic conditions affecting the freshwater and marine environments during the last century. Different geographic and life history components that were minor producers during one climatic regime have dominated during others, emphasizing that the biocomplexity of fish stocks is critical for maintaining their resilience to environmental change.

Alaska↗
PubMed2024

Extreme elevational migration spurred cryptic speciation in giant hummingbirds.

The ecoevolutionary drivers of species niche expansion or contraction are critical for biodiversity but challenging to infer. Niche expansion may be promoted by local adaptation or constrained by physiological performance trade-offs. For birds, evolutionary shifts in migratory behavior permit the broadening of the climatic niche by expansion into varied, seasonal environments. Broader niches can be short-lived if diversifying selection and geography promote speciation and niche subdivision across climatic gradients. To illuminate niche breadth dynamics, we can ask how "outlier" species defy constraints. Of the 363 hummingbird species, the giant hummingbird (Patagona gigas) has the broadest climatic niche by a large margin. To test the roles of migratory behavior, performance trade-offs, and genetic structure in maintaining its exceptional niche breadth, we studied its movements, respiratory traits, and population genomics. Satellite and light-level geolocator tracks revealed an >8,300-km loop migration over the Central Andean Plateau. This migration included a 3-wk, ~4,100-m ascent punctuated by upward bursts and pauses, resembling the acclimatization routines of human mountain climbers, and accompanied by surging blood-hemoglobin concentrations. Extreme migration was accompanied by deep genomic divergence from high-elevation resident populations, with decisive postzygotic barriers to gene flow. The two forms occur side-by-side but differ almost imperceptibly in size, plumage, and respiratory traits. The high-elevation resident taxon is the world's largest hummingbird, a previously undiscovered species that we describe and name here. The giant hummingbirds demonstrate evolutionary limits on niche breadth: when the ancestral niche expanded due to evolution (or loss) of an extreme migratory behavior, speciation followed.

Animals↗
PubMed2024

Rapid vertebrate speciation via isolation, bottlenecks, and drift.

Speciation is often driven by selective processes like those associated with viability, mate choice, or local adaptation, and "speciation genes" have been identified in many eukaryotic lineages. In contrast, neutral processes are rarely considered as the primary drivers of speciation, especially over short evolutionary timeframes. Here, we describe a rapid vertebrate speciation event driven primarily by genetic drift. The White Sands pupfish (Cyprinodon tularosa) is endemic to New Mexico's Tularosa Basin where the species is currently managed as two Evolutionarily significant units (ESUs) and is of international conservation concern (Endangered). Whole-genome resequencing data from each ESU showed remarkably high and uniform levels of differentiation across the entire genome (global FST ≈ 0.40). Despite inhabiting ecologically dissimilar springs and streams, our whole-genome analysis revealed no discrete islands of divergence indicative of strong selection, even when we focused on an array of candidate genes. Demographic modeling of the joint allele frequency spectrum indicates the two ESUs split only ~4 to 5 kya and that both ESUs have undergone major bottlenecks within the last 2.5 millennia. Our results indicate the genome-wide disparities between the two ESUs are not driven by divergent selection but by neutral drift due to small population sizes, geographic isolation, and repeated bottlenecks. While rapid speciation is often driven by natural or sexual selection, here we show that isolation and drift have led to speciation within a few thousand generations. We discuss these evolutionary insights in light of the conservation management challenges they pose.

Animals↗
PubMed1993

Disease risk as a cost of outbreeding in the termite Zootermopsis angusticollis.

The effect of the sibship of primary reproductives on mate mortality and the survivorship and growth of incipient colonies was studied in the dampwood termite Zootermopsis angusticollis. Males and females paired with nonsibling mates had higher mortality during the first 10-40 days after pairing, although male and female reproductives showed similar patterns of mortality after colony establishment. The source of mortality appeared to be fungal and/or bacterial pathogens. There were no overall differences in the number of eggs and larvae produced by sibling and nonsibling pairs, and no differences in colony size and biomass 4 years after colony establishment. We therefore could not identify any negative effect of inbreeding in the early phases of colony development. Our results suggest that the risk of exposure to pathogens and the ability of termites to locally adapt to disease could influence the genetic identity of primary reproductives and the extent of inbreeding in termite populations.

Journal Article↗
PubMed1999

Mechanisms of color constancy under nearly natural viewing.

Color constancy is our ability to perceive constant surface colors despite changes in illumination. Although color constancy has been studied extensively, its mechanisms are still largely unknown. Three classic hypotheses are that constancy is mediated by local adaptation, by adaptation to the spatial mean of the image, or by adaptation to the most intense image region. We measure color constancy under nearly natural viewing conditions, by using a design that allows us to test these three hypotheses directly. By suitable stimulus manipulation, we are able to titrate the degree of constancy between 11% and 83%, indicating that we have achieved good laboratory control. Our results rule out all three classic hypotheses and thus suggest that there is more to constancy than can be easily explained by the action of simple visual mechanisms.

Adaptation, Biological↗
PubMed2004

Changing the individual to promote health-enhancing physical activity: the difficulties of producing evidence and translating it into practice.

This paper presents conclusions from recent systematic reviews and highlights individually targeted interventions that are effective at increasing physical activity. It discusses the limitations of currently available evidence, considers what factors lead to these limitations and what barriers exist in terms of implementing the evidence as part of local and national policy and practice. Barriers present themselves in terms of getting evidence into practice and in terms of ensuring that practice informs the evidence base. These barriers include difficulties in conducting systematic reviews, disaggregating knowledge from complex interventions, making local adaptations to existing evidence, the lack of an evaluation culture, ethical and pragmatic difficulties in designing interventions, selecting appropriate outcome measures, poor designs and implementation of evidence and, finally, a recognition that policy making is not only based on the available evidence. New and more integrated approaches to evaluation and to practice are needed.

Community Health Services↗
PubMed2005

Magnetic resonance temperature imaging.

Continuous, real-time, 3D temperature mapping during a hyperthermic procedure may provide (i) enhanced safety by visualizing temperature maps in and around the treated region, (ii) improved efficiency by adapting local energy deposition with feedback coupling algorithms and (iii) therapy end-points based on the accumulated thermal dose. Non-invasive mapping of temperature changes can be achieved with MRI and may be based on temperature dependent MRI parameters. The excellent linearity of the temperature dependency of the proton resonance frequency (PRF) and its near-independence with respect to tissue type make the PRF-based methods the preferred choice for many applications, in particular at mid- to-high field strength (> or =0.5 T). The PRF methods employ RF-spoiled gradient echo imaging methods and incorporate fat suppression techniques for most organs. A standard deviation of less than 1 degrees C, for a temporal resolution below 1 s and a spatial resolution of approximately 2 mm is feasible for immobile tissues. Special attention is paid to methods for reducing artifacts in MR temperature mapping caused by intra-scan and inter-scan motion and motion and temperature-induced susceptibility effects in mobile tissues. Real-time image processing and visualization techniques, together with accelerated MRI acquisition techniques, are described because of their potential for therapy guidance.

Humans↗
PubMed1999

Proximal Femoral Density Patterns are Consistent with Bicentric Joint Loads.

We developed an alternate method for density-based load estimation and applied it to estimate hip joint load distributions for two femora. Two-dimensional finite element models were constructed from single energy quantitative computed tomography (QCT) data. Load estimation was performed using five loading regions on the femoral head. Within each loading region, individual nodal loads, normal to the local surface, were supplied as input to the load estimation. An optimization procedure independently adjusted individual nodal load magnitudes in each region, and the magnitudes of muscle forces on the greater trochanter, such that the applied tissue stimulus approached the reference stimulus throughout the model. Dominant estimated load resultant directions were generally consistent with published experimental data for loads during gait. The estimated loads also suggested that loads near the extremes of the articulating surface may be important (even required) for development and maintenance of normal bone architecture. Estimated load distributions within nearly all regions predicted bicentric loading patterns, which are consistent with observations of hip joint incongruity. Remodeling simulations with the estimated loads predicted density distributions with features qualitatively similar to the QCT data sets. This study illustrates how applications of density-based bone load estimation can improve understanding of dominant loading patterns in other bones and joints. The prediction of bicentric loading suggests a very fine level of local adaptation to details of joint loading.

Journal Article↗
PubMed2004

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

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

Animals↗