Francisco B.-G. Moore

Population structure of spotted salamanders (Ambystoma maculatum) in a fragmented landscape

Understanding the impacts of landscape‐level processes on the population biology of amphibians is critical, especially for species inhabiting anthropogenically modified landscapes. Many pond‐breeding amphibians are presumed to exist as metapopulations, but few studies demonstrate the extent and consequences of this metapopulation structure. Gene flow measures may facilitate the construction of more realistic models of population structure than direct measures of migration. This is especially true for species that are cryptic, such as many amphibians. We used eight polymorphic microsatellite loci to determine the genetic population structure of spotted salamanders (Ambystoma maculatum) breeding at 17 ponds in northeastern Ohio, a landscape fragmented by roads, agriculture, urban areas and the Cuyahoga River. Using a variety of analyses (Bayesian clustering, F‐statistics, AMOVA) we generated a model of salamander population genetic structure. Our data revealed patterns of genetic connectivity that were not predicted by geographical distances between ponds (no isolation by distance). We also tested for a relationship between population structure and several indices of landscape resistance, but found no effect of potential barriers to dispersal on genetic connectivity. Strong overall connectivity among ponds, despite the hostile habitat matrix, may be facilitated by a network of riparian corridors associated with the Cuyahoga River; however, high gene flow in this system may indicate a general ability to disperse and colonize beyond particular corridors.

The Environment Affects Epistatic Interactions to Alter the Topology of an Empirical Fitness Landscape

The fitness effect of mutations can be influenced by their interactions with the environment, other mutations, or both. Previously, we constructed 32 ( = 25) genotypes that comprise all possible combinations of the first five beneficial mutations to fix in a laboratory-evolved population of Escherichia coli. We found that (i) all five mutations were beneficial for the background on which they occurred; (ii) interactions between mutations drove a diminishing returns type epistasis, whereby epistasis became increasingly antagonistic as the expected fitness of a genotype increased; and (iii) the adaptive landscape revealed by the mutation combinations was smooth, having a single global fitness peak. Here we examine how the environment influences epistasis by determining the interactions between the same mutations in two alternative environments, selected from among 1,920 screened environments, that produced the largest increase or decrease in fitness of the most derived genotype. Some general features of the interactions were consistent: mutations tended to remain beneficial and the overall pattern of epistasis was of diminishing returns. Other features depended on the environment; in particular, several mutations were deleterious when added to specific genotypes, indicating the presence of antagonistic interactions that were absent in the original selection environment. Antagonism was not caused by consistent pleiotropic effects of individual mutations but rather by changing interactions between mutations. Our results demonstrate that understanding adaptation in changing environments will require consideration of the combined effect of epistasis and pleiotropy across environments.

Developmental Environment Alters Conditional Aggression in Zebrafish

Abstract The developmental environment influences a wide variety of phenotypic traits in the adults of many vertebrates (i.e., developmental plasticity). In this study, we test to see if developmental environment (EDEV) interacts with the adult behavioral environment (EBEHAV) in determining behavioral phenotypes. We reared Zebrafish (Danio rerio) from eggs in either continuously hypoxic or normoxic conditions. We then tested aggression and avoidance (i.e., hiding) levels of fish from each developmental treatment in both environments. Developmental environment was a significant source of variation in avoidance behavior while the stimulus environment did not influence avoidance. Without a period of acclimation we found that EBEHAV and an EDEV × EBEHAV interaction were both significant sources of variation. However, when the fish were allowed to physiologically acclimate to the environment for 16 h, aggression level was highest for fish tested in the environment in which they developed. In that case the EDEV × EBEHAV interaction was the only significant source of variation. These results demonstrate that a more complete understanding of phenotypic response can be gained by incorporating environmental conditions across multiple time scales.

A SIMULATION OF WRIGHT'S SHIFTING-BALANCE PROCESS: MIGRATION AND THE THREE PHASES

Wright partitioned the shifting‐balance process into three phases. Phase one is the shift of a deme within a population to the domain of a higher adaptive peak from that of the historical peak. Phase two is mass selection within a deme towards that higher peak. Phase three is the conversion of additional demes to the higher peak. The migration rate between demes is critical for the existence of phases one and three. Phase one requires small effective population sizes, hence low migration rates. Phase three is optimal under high migration rates that spread the most‐fit genotype from deme to deme. Thus, a population‐wide peak shift requires intermediate levels of migration. By altering the rates of phases one and three, migration affects the predominant direction of mass selection within a population. This study examines the degree to which migration, through its effects on phases one and three, determines the probability of a simulated population arriving at its genotypic optimum after 12,000 generations. These simulations reveal that there is a range of migration rates for which an entire population might be expected to shift to a higher peak. Below m = 0.001 peak shifts occur frequently (phases I and II) but are not successfully exported out of subpopulations (phase III), and above 0.01 peak shifts within demes (phase I and II), required to initiate phase III, become increasingly uncommon. Because it is unlikely that real populations will have uniform migration rates from generation to generation, the probable effects of varying migration rates on broadening the range of conditions producing peak shifts are discussed.

The role of thermal niche selection in maintenance of a colour polymorphism in redback salamanders (Plethodon cinereus)

BackgroundIn eastern North America two common colour morphs exist in most populations of redback salamanders (Plethodon cinereus). Previous studies have indicated that the different morphs may be adapted to different thermal niches and the morphological variation has been linked to standard metabolic rate at 15°C in one population of P. cinereus. It has therefore been hypothesized that a correlated response to selection on metabolic rate across thermal niches maintains the colour polymorphism in P. cinereus. This study tests that hypothesis.ResultsWe found that the two colour morphs do sometimes differ in their maintenance metabolic rate (MMR) profiles, but that the pattern is not consistent across populations or seasons. We also found that when MMR profiles differ between morphs those differences do not indicate that distinct niches exist. Field censuses showed that the two colour morphs are sometimes found at different substrate temperatures and that this difference is also dependent on census location and season.ConclusionWhile these morphs sometimes differ in their maintenance energy expenditures, the differences in MMR profile in this study are not consistent with maintenance of the polymorphism via a simple correlated response to selection across multiple niches. When present, differences in MMR profile do not indicate the existence of multiple thermal niches that consistently mirror colour polymorphism. We suggest that while a relationship between colour morph and thermal niche selection appears to exist it is neither simple nor consistent.

Pervasive RNA Editing Among Hornwort rbcL Transcripts Except Leiosporoceros

RNA editing affecting chloroplast and mitochondrial genomes has been identified in all major clades of land plants. The frequency of edited sites varies greatly between lineages but hornworts represent an extreme in propensity for editing in both their chloroplast and mitochondrial genomes. cDNA sequences from seven taxonomically diverse hornwort rbcL sequences combined with a survey of 13 additional DNA sequences for potential edited sites demonstrate the presence of 62 edited sites and predict a minimum of 10 additional sites. These 72 total edited sites represent 43 C-to-U and 28 U-to-C nucleotide conversions, with 1 site exhibiting editing in both directions. With one exception, all taxa are heavily edited, with each having from 20 to 34 edited sites. However, a single sample, Leiosporoceros, is shown to lack edited sites. Phylogenetic reconstruction of hornworts results in ambiguous resolution of Leiosporoceros depending on whether edited sites are maintained or eliminated from the analyses. Depending on the inferred relationship of Leiosporoceros to the hornworts, at least two explanations for the origin and maintenance of pervasive editing in hornworts are possible. The absence of edited sites in Leiosporoceros could represent either the absence or a low level of editing ability in the common ancestor of hornworts, as represented by Leiosporoceros, or the loss of editing sites in this lineage after the primary diversification events in the group.

Cardiovascular system in larval zebrafish responds to developmental hypoxia in a family specific manner

BackgroundGenetic and environmental variation are both known to influence development. Evolution of a developmental response that is optimized to the environment (adaptive plasticity) requires the existence of genetic variation for that developmental response. In complex traits composed of integrated sets of subsidiary traits, the adaptive process may be slowed by the existence of multiple possible integrated responses. This study tests for family (sibship) specific differences in plastic response to hypoxia in an integrated set of cardiovascular traits in zebrafish.ResultsCardiac output, which is the integrated product of several subsidiary traits, varied highly significantly between families, and families differed significantly in the degree and direction of response to developmental oxygen level. The cardiac output response to oxygen environment was entirely family specific with no significant overall trend due to oxygen level. Constituent physiological variables that contribute to cardiac output all showed significant family specific response to hypoxia. Traits that were not directly related to cardiac output, such as arterial and venous diameter, and red blood cell velocities did not respond to hypoxia in a family specific manner.ConclusionZebrafish families vary in their plastic response to hypoxia. Genetic variation in plastic response to hypoxia may therefore provide the basic ingredient for adaptation to a variable environment. Considerable variation in the degree of familial response to hypoxia exists between different cardiovascular traits that may contribute to cardiac output. It is possible that the integration of several subsidiary traits into cardiac output allows the maintenance of genetic variance in cardiac response.

J-LEAPS vaccines initiate murine Th1 responses by activating dendritic cells.

The Ligand Epitope Antigen Presentation System (LEAPS) converts a peptide containing a T cell epitope as small as 8 amino acids into an immunogen and directs the nature of the subsequent response. Tandem synthesis of the J peptide (a peptide from the beta-2-microglobulin) with peptides of 15 or 30 amino acids from HSV-1 or HIV made them immunogenic and promoted Th1 immune responses. Immunization of A/J or C57BL/6 mice with J-LEAPS heteroconjugates containing an epitope from the HSV-1 glycoprotein D (JgD) or an epitope from the HIV gag protein (JH) emulsified with Seppic ISA51 induced increased levels of IL-12p70 by day 3 and increased levels of interferon gamma (IFN-gamma) on days 10 and 24. Interestingly, levels of IL-10, TNF-alpha, and IL-6 did not change. Neither the H nor the gD peptides alone elicited responses and only weak responses followed immunization with the J peptide. Bone marrow (BM) cells became CD86 and CD11c positive within 48 h of treatment with JgD or JH. JH or JgD treatment promoted IL-12p70 production and expression of CD8 denoting the maturation and activation of a subclass of myeloid DCs. Pure cultures of immature myeloid DCs also responded to JgD treatment, forming clusters, developing dendrites, and producing IL-12p70 within 24 h. The JH or JgD treated bone marrow cells (JgD-DC) were necessary and sufficient to activate splenic T cells to produce IFN-gamma and the JgD-DC provided an antigen specific booster response to T cells from JgD immunized mice. Adoptive transfer of JgD-DC was also sufficient to initiate protective antigen specific immunity from lethal challenge with HSV-1. The J-LEAPS vaccines appear to act as an adjuvant and immunogen on DC precursors in a unique manner to promote activation and maturation into IL-12p70 producing DCs which then can initiate sufficient Th1 immune responses to elicit protection without production of acute phase cytokines.

Ontogenetic oxygen changes alter zebra fish size, behavior, and blood glucose.

Four male and four female zebra fish were crossed in all possible combinations, resulting in 389 offspring. These offspring were divided among four treatments: normoxia for 90 d, hypoxia for 90 d, normoxia for 30 d followed by hypoxia for 60 d, and hypoxia for 30 d followed by normoxia for 60 d. The effects of early oxygen environment, later oxygen environment, and genotype were then assessed with respect to zebra fish behavior, size, and blood glucose. Fish were tested in an arena where they could shoal with conspecifics before, during, and after the introduction of a novel stimulus. Blood glucose and size were also measured. Early oxygen environment influenced fish size, time spent swimming, and reactivity to a novel stimulus. Environmentally induced plasticity was predominate, with little evidence of among-sire variation for any of the measured parameters.

A weighted k-nearest neighbor method for gene ontology based protein function prediction

Numerous genome projects have produced a large and ever increasing amount of genomic sequence data. However, the biological functions of many proteins encoded by the sequences remain unknown. Protein function annotation and prediction become an essential and challenging task of post-genomic research. In this paper, we present an automated protein function prediction system based on a set of proteins of known biological functions. The functions of the proteins are characterized with gene ontology (GO) annotations. The prediction system uses a novel measure to calculate the pair-wise overall similarity between protein sequences. The protein function prediction is performed based on the GO annotations of similar sequences using a weighted k-nearest neighbor method. We show the prediction accuracies obtained using the model organism yeast (Sacchyromyces cerevisiae). The results indicate that the weighted k-nearest neighbor method significantly outperforms the regular k-nearest neighbor method for protein molecular function prediction.In tennis competition, there are some reasons leading to the competition results inaccurately. So I put forward a real-time competition simulation system to solve the tennis problem. It can overcome the limitations and the blind spots that occur in human observation. The system includes four parts: image collection, moving object detection and tracking, static scene simulation, competition simulation. This paper presents an algorithm for the detection and tracking of moving objects in sequence images that can be applied in simulations of tennis competition. The approach differs from most other methods that solve the problems of object occlusion and object deformation. The experimental results proved that our method is feasibility and usefulness.