Intron-targeted PCR: a new approach to survey neutral DNA polymorphism in bivalve populations

PCR (polymerase chain reaction) amplification of non-coding introns in phylogenetically widespread genes, using DNA primers based on the conserved exon sequences, provides a widely applicable strategy for finding DNA polymorphisms in eukaryotic genomes. Polymorphisms in introns provide a new source of potentially neurtral genetic markers for use in population biology. Here we use this approach to design PCR primers for an intron of calmodulin genes. We show that there are at least two calmodulin genes in mussels of theMytilus edulis species complex, and using gene- and species-specific primers we resolve two alleles at a calmodulin intron locus. Population surveys using PcR of adult mussel DNA reveal that genotype frequencies at most sites surveyed in England, Scotland and Italy, conform to Hardy-Weinberg equilibrium, suggesting that this is a novel neutral genetic marker. The data also provide preliminary evidence for restricted gene flow between mussel populations on the west and northeast coasts of Britain, and for local effects around the Thames estuary.     

Dynamic zonation of Nerita plicata,N. undata and N. textilis (Prosobranchia: Neritacea) populations on a rocky shore in Kenya

Vertical zonation of Nerita plicata Linnaeus, N. undata Linnaeus, and N. textilis Dillwyn, inhabiting the rocky cliffs of Nyali, Kenya, was studied through several spring-neap tidal cycles from November to December (northeastern monsoon) 1981 and May to July (southeastern monsoon) 1982. For the first time, a monsoon-related cycle of migration in Nerita plicata and N. undata, superimposed on the shorter term spring-neap cycle is demonstrated. Both species rest predominantly in the upper eulittoral zone and the littoral fringe. N. plicata and N. undata rest at significantly higher levels during the southeastern monsoon (SEM) than during the northeastern monsoon (NEM) (P<0.001). On and around neap-tide days N. plicata, N. undata, and N. textilis occupy significantly distinct mean resting positions (P<0.001) in both seasons; N. undata being the highest in the SEM, followed by N. plicata, with N. textilis always in the lowest level. In the NEM, N. plicata and N. undata sometimes change order. On and around springtide days in both seasons, the upper two species, N. plicata and N. undata, rest close together with no significant difference in their mean resting positions, but with both significantly higher than N. textilis (P<0.001). Both the spring-neap and the monsoon migrations of N. plicata and N. undata are interpreted as either direct or indirect responses to wave action.     

Genetic structure of hybrid mussel populations in the west of Ireland: two hypotheses revisited

In Ireland, mussels on exposed rocky shores constitute an interbreeding mixture of two forms of mussels, the blue mussel, Mytilus edulis, and the Mediterranean mussel, M. galloprovincialis. Results from an Irish study in the 1980s, using partially diagnostic allozyme markers, indicated that mussels higher up the shore were more galloprovincialis-like than those lower down. In this study we set out to test two hypotheses: (a) recruits arriving on the shore are composed of genetically distinct cohorts that settle preferentially at different levels on the shore, and maintain genetic distinctiveness into adulthood; (b) recruits are genetically homogeneous, but once settled they diverge genetically over time, due to within-habitat site specific-selection. The diagnostic Me 15/16 DNA marker was used to analyse the genetic composition of newly-settled spat recruiting to artificial substrates, which were placed at two-week intervals from May–October 2002, on the mid- and low shore areas of two exposed sites in Galway Bay. Adult mussels were also collected on each sampling date. Results did not support the preferential settlement hypothesis, i.e., the genetic composition of primary settlers (≤ 500 μm) was similar between tidal heights and shores. Neither was there evidence of post settlement selective mortality, as adults were genetically similar to settling spat. In spat and adults the frequency of the M. galloprovincialis allele was high (0.56–0.80), due to high frequencies of M. galloprovincialis (> 37%) and hybrid (> 33%) genotypes, and correspondingly low frequencies of the M. edulis genotype (< 11%). Adult mussels from a nearby sheltered estuarine site, while significantly different to exposed shore mussels, still had low frequencies of the M. edulis genotype (< 17%), indicating no apparent advantage for the genotype in this environment. There are indications that the genetic composition of mussels may be changing on the Atlantic coasts of Ireland.     

Genotype-dependent fecundity and temporal variation of spawning in hybrid mussel (Mytilus) populations

Mussel samples were collected at 4 to 6 wk intervals throughout 1987 from two hybridMytilus edulis/M. galloprovincialis populations, at Croyde Bay and Whitsand Bay, in southwest England. These were analyzed at two polymorphic loci which are diagnostic for allozyme differences which typifyM. edulis andM. galloprovincialis. Dry mantle weight as a function of shell length was determined for all individuals of each sample. Size-frequency data for the two populations was obtained in September 1987 and March 1988. For all genotypes at both sites, fecundity was a function of shell length, and in both populations the frequency ofM. galloprovincialis alleles was positively correlated with shell length. At both sites, allozyme genotype explained a significant amount of variation in mantle weight either when assessed as a main effect or when assessed as an interaction with shell length or time of collection. At Croyde,M. galloprovincialis mussels had greater estimated fecundity per unit length than theM. edulis mussels. Differences in the timing of spawning activity between theM. edulis and theM. galloprovincialis mussels were inferred, and these differences might act to reduce the amount of interbreeding at Croyde. At Whitsand, a reduced level of variability in the timing of spawning activity and fecundity between the genotypes was observed and explained by a higher degree of genetic mixing. Because theM. galloprovincialis mussels had (1) a greater estimated fecundity at any length, and (2) a greater mean length than theM. edulis mussels, the mean genotypic annual fecundity perM. galloprovincialis mussel was 2.8 times greater than an individualM. edulis mussel at Croyde, and 2.2 times greater than an individualM. edulis mussel at Whitsand. This evidence thatM. galloprovincialis mussels have an advantage in fecundity, and thus perhaps in fertility, taken together with the evidence thatM. galloprovincialis also has a higher viability, indicates directional selection in favour of theM. galloprovincialis phenotype. Because of the observed temporal stability of the population it seems likely that this selection is counterbalanced by a massive imigration ofM. edulis spat from neighbouring populations.     

Shell shape variation in populations of Mytilus chilensis (Hupe 1854) from southern Chile: a geometric morphometric approach

The pattern of shell shape variation in populations of the mussel, Mytilus chilensis (Hupe 1854) from Southern Chile was analyzed as a function of sample origin (cultivated vs. wild) and latitude, using standard tools of geometric morphometrics for landmark data. Additionally, posterior adductor muscle index (PAMI), Freeman condition index and shell thickness were measured in each sample. Highly significant differences in shell shape components were found among mussel populations. These differences are related to the origin of samples (expansion of the posterior adductor muscle scar, elongation of the lateral ligament and of the ventral umbo position in non-cultivated samples) and to latitude (more elongated shells and more extended posterior adductor muscle scar in most southern samples when compared with the northernmost ones). PAMI and shell thickness were statistically higher in wild population, and Freeman condition index was higher in cultivated shells. It is suggested that in wild populations of M. chilensis, the mussels may face higher predator pressures and other environmental stress factors. Consequently, individuals may be using higher energy fraction to reinforce shells and to promote adductor muscle growth at the expense of somatic growth. In contrast, individuals found in calm aquaculture environments are relatively protected from predators and use most of their assimilated energy in somatic growth. In turn, this growth depends on changes that covariate with shell morphology.     

The response of the woodpigeon (Columba palumbus) to relaxation of intraspecific competition: A hybrid modelling approach

The recent rapid growth of the woodpigeon population in the British Isles is a cause for concern for environmental managers. It is unclear what has driven their increase in abundance. Using a mathematical model, we explored two possible mechanisms, reduced intraspecific competition for food and increased reproductive success. We developed an age-structured hybrid model consisting of a system of ordinary differential equations that describes density-dependent mortality and a discrete component, which represents the birth-pulse. We investigated equilibrium population dynamics using our model. The two hypotheses predict contrasting population age profiles at equilibrium. We adapted the model to examine the impacts of control measures. We showed that an annual shooting season that follows the period of density-dependent mortality is the most effective control strategy because it simultaneously removes adult and juvenile woodpigeons. The model is a first step towards understanding the processes that influence the dynamics of woodpigeon populations.     

On interacting bee/mite populations: a stochastic model with analysis using cumulant truncation

Parasitism by the Varroa mite has had recent drastic impact on both managed and feral bee colonies. This paper proposes a stochastic population dynamics model for interacting African bee colony and Varroa mite populations. Cumulant truncation procedures are used to obtain approximate transient cumulant functions, unconstrained by the usual assumption of bivariate Normality, for an assumed large-scale model. The apparent size of the variance and skewness functions suggest the importance of the proposed truncation procedure which retains some higher-order cumulants, but determining the accuracy of the approximations is problematical. A smaller-scale bee/Varroa mite model is hence proposed and investigated. The accuracy for the means is exceptional, for the second-order cumulants is moderate, and for some third-order cumulants is poor. Notwithstanding the poor accuracy of a skewness approximation, the saddlepoint approximations for the marginal transient population size distributions are excellent. The cumulant truncation methodology is very general, and research is continuing in its application to this new class of host-parasite models.     

Temporal patterns of populations in a warming world: a modelling framework

In this paper, we present an approach for describing the environmentally induced temporal pattern of structured populations by partial integro-differential equations. Populations are structured according to size or stage. Growth, energy allocation and stage transitions are affected by environmental conditions of which temperature, photoperiod, water depth and food supply were taken into account. The resulting modelling framework was applied to describe, analyse and predict alterations in populations with continuous development, populations with distinct state structures and interacting populations. Our exemplary applications consider populations of freshwater Amphipoda, Isopoda and Odonata. The model was capable of simulating life cycle alterations in dependence on temperature in interaction with other environmental factors: (1) population dynamics, (2) seasonal regulation, (3) water depth-dependent dispersal, (4) intraguild predation and (5) consumer-resource dynamics.     

Two-dimensional hybrid perovskite solar cells: a review

The production of electricity is important, suitable and secure for human living, yet electricity is actually generated mainly from fossil fuels and nuclear energy, calling for renewable energies such as solar, wind and tidal renewable energies such as solar, wind and tidal. Solar energy is broadly harvested by various types of solar cells. Three-dimensional perovskite solar cell exhibits high power conversion efficiency of 25.2% with low stability, whereas two-dimensional perovskite solar cell exhibits better stability with moderate power conversion efficiency. Hence, we review two-dimensional perovskite solar cells fabricated with varying numbers of hybrid two-dimensional perovskite layers, organic cations, deposition techniques, the addition of additives and capping layers to improve power conversion efficiency with long-term better stability.

     

Forecasting industrial emissions: a monetary approach vs. a physical approach

Forecasts of industrial emissions provide a basis for impact assessment and development planning. To date, most studies have assumed that industrial emissions are simply coupled to production value at a given stage of technical progress. It has been argued that the monetary method tends to overestimate pollution loads because it is highly influenced by market prices and fails to address spatial development schemes. This article develops a land use-based environmental performance index (L-EPI) that treats the industrial land areas as a dependent variable for pollution emissions. The basic assumption of the method is that at a planning level, industrial land use change can represent the change in industrial structure and production yield. This physical metric provides a connection between the state-of-the-art and potential impacts of future development and thus avoids the intrinsic pitfalls of the industrial Gross Domestic Product-based approach. Both methods were applied to examine future industrial emissions at the planning area of Dalian Municipality, North-west China, under a development scheme provided by the urban master plan. The results suggested that the LEPI method is highly reliable and applicable for the estimation and explanation of the spatial variation associated with industrial emissions.     

Defining length-at-metamorphosis in fishes: a multi-character approach

The present study attempts to highlight the value of multi-character approaches for defining thresholds in fish ontogeny, like the onset of the juvenile period. We developed techniques to objectively define the transition from larval to juvenile development using morphometric as well as morphological characters and exemplify the multi-character approach on newly settled white sea-breams (Diplodus sargus sargus) collected from the eastern Mediterranean. The morphometric analysis was based on principles of multivariate allometry whereas the analysis of morphology, on assigning a suite of selected characters (here related to external morphology and osteological development) into larval, transforming and juvenile states. The size-at-change in multivariate allometric growth (L _m) is considered here to denote mean length-at-metamorphosis. An almost perfect match is demonstrated between L _m (‘multivariate morphometry’) and mean size-at-morphological change (‘multivariate morphology’) in white sea-bream.     

Longleaf pine (Pinus palustris) and hardwood dynamics in a fire-maintained ecosystem: A simulation approach

Longleaf pine (Pinus palustris) savannas of the southeastern U.S. represent an archetype of a fire dependent ecosystem. They are known to have very short fire return intervals (∼1-3 years) that perpetuate understory plant diversity (up to 50 species m⁻²), support pine recruitment, and suppress fire sensitive hardwoods. Understanding the relationships that regulate longleaf and southern hardwoods is especially critical. With decreased fire frequency, insufficient intensity, or lack of underground competition, a woody mid-story rapidly develops, dominated by fire sensitive trees and shrubs that in-turn suppress more fire dependent species (including pine seedlings). This may occur in forest gaps, where pine-needle abundance is diminished, reducing fire spread potential. The interactions between longleaf pine, hardwoods, forest fuels, and fire frequency are complex and difficult to understand spatially. The objective of this study was to develop a spatially explicit longleaf pine-hardwood stochastic simulation model (LLM), incorporating tree demography, plant competition, and fuel and fire characteristics. Data from two longleaf pine study sites were used to develop and evaluate the model with the goal to incorporate simple site-specific calibration parameters for model versatility. Specific model components included pine seed masting, hardwood clonal sprouting, response to fire (re-sprouting, mortality), and tree density driven competition effects. LLM spatial outputs were consistent with observed forest gap dynamics associated with pine seedling establishment and hardwood encroachment. Changes in fire frequency (i.e., fire probability = 0.35-0.05) illustrated a shift in community structure from longleaf pine dominated to a hardwood dominated community. This approach to assessing model response may be useful in characterizing longleaf ecosystem resilience, especially at intermediate fire frequencies (e.g., 0.15) where the community may be sensitive to small changes in the fire regime. Height distributions and population densities were similar to in situ findings (field and LIDAR data) for both study sites. Height distributions output by the LLM illustrated fluctuations in population structure. The LLM was especially useful in determining knowledge gaps associated with fuel and fire heterogeneity, plant-plant interactions, population structure and its temporal fluctuations, and hardwood demography. This is the first known modeling work to simulate interactions between longleaf pine and hardwoods and provides a foundation for further studies on fire and forest management, especially in relation to ecological forestry practices, restoration, and site-specific applications.     

Sink populations in carnivore management: cougar demography and immigration in a hunted population.

Carnivores are widely hunted for both sport and population control, especially where they conflict with human interests. It is widely believed that sport hunting is effective in reducing carnivore populations and related human-carnivore conflicts, while maintaining viable populations. However, the way in which carnivore populations respond to harvest can vary greatly depending on their social structure, reproductive strategies, and dispersal patterns. For example, hunted cougar (Puma concolor) populations have shown a great degree of resiliency. Although hunting cougars on a broad geographic scale (> 2000 km2) has reduced densities, hunting of smaller areas (i.e., game management units, < 1000 km2), could conceivably fail because of increased immigration from adjacent source areas. We monitored a heavily hunted population from 2001 to 2006 to test for the effects of hunting at a small scale (< 1000 km2) and to gauge whether population control was achieved (lambda < or = 1.0) or if hunting losses were negated by increased immigration allowing the population to remain stable or increase (lambda > or = 1.0). The observed growth rate of 1.00 was significantly higher than our predicted survival/fecundity growth rates (using a Leslie matrix) of 0.89 (deterministic) and 0.84 (stochastic), with the difference representing an 11-16% annual immigration rate. We observed no decline in density of the total population or the adult population, but a significant decrease in the average age of independent males. We found that the male component of the population was increasing (observed male population growth rate, lambda(OM) = 1.09), masking a decrease in the female component (lambda(OF) = 0.91). Our data support the compensatory immigration sink hypothesis; cougar removal in small game management areas (< 1000 km2) increased immigration and recruitment of younger animals from adjacent areas, resulting in little or no reduction in local cougar densities and a shift in population structure toward younger animals. Hunting in high-quality habitats may create an attractive sink, leading to misinterpretation of population trends and masking population declines in the sink and surrounding source areas.     

Complex courtship in a bimodal grasshopper hybrid zone

Grasshoppers of the Chorthippus albomarginatus-group, which is outstanding with respect to its complex courtship song, were studied at fifteen localities in the Ukraine and Moldova. The analysis of the courtship songs revealed two species: C. albomarginatus in north-eastern Ukraine and Chorthippus oschei in the south-western Ukraine and Moldova. In a belt about 200 km wide, not only were one or the other pure species found, but also males with intermediate song characters. C. albomarginatus and C. oschei were hybridised in the laboratory, and F1 hybrid males as well as F2 hybrid males produced intermediate song patterns, quite similar to those recorded in the field. We defined a "hybrid song score" for intermediate songs. The score showed a bimodal distribution with most songs resembling one or other parental type, but with only a few intermediates. At several localities, where hybrids with songs similar to one of the parental species dominated, some individual males sang more similarly to the other species. In one locality, two hybrid populations only 3 km apart had different parental types. Hybrid songs can contain novel elements, even more complex than the parental ones, which may offer a new starting point for sexual selection. We suggest that genetic introgression occurs between the two sibling species C. albomarginatus and C. oschei within a wide hybrid zone stretching over a distance of several hundred kilometres, but with a patchy spatial distribution. Electronic Supplementary Material Supplementary material is available for this article if you access the article at . A link in the frame on the left on that page takes you directly to the supplementary material. Communicated by D. Gwynne     

Variation in strength of attachment to the substrate explains differential mortality in hybrid mussel (Mytilus galloprovincialis and M. edulis) populations

Mussel samples were collected from a hybrid mussel (Mytilus galloprovincialis and M. edulis) Population at Croyde, southwest England, in January, March and May 1990. The strength of attachment of each mussel to the substrate was measured with a spring balance. A number of diagnostic characters were also recorded. These are shell lengh, width and height, mantle colour and genotype at two allozyme loci, esterase-D and octopine dehydrogenase. Multiple-regression analysis was used to assess the effect of the diagnostic characters on strength of attachment as dependent variable. Mussels possessing the relatively high shells and darker mantle colouration characteristic of M. galloprovincialis had higher values, on average, for strength of attachment than mussels resembling M. edulis. Phenotypically intermediate mussels had intermediate values for strength of attachment. The results suggest an adaptive difference which can account for reports of differential mortality acting in favour of M. galloprovincialiis.     

Growth maximization in early sardine larvae: a metabolic approach

Sardine larvae are forced to grow as fast as possible to reduce larval mortality. Thus, changes in biochemical composition during the first steps of sardine larval growth are intended to maximize larval growth rate efficiency and survival. Protein and RNA weight-specific growth rates were the highest and their corresponding doubling times the shortest among all the biomolecules, reflecting the importance of fast growth during early stages of larval development. The protein percentage increased and the carbohydrate and lipid percentages decreased during early growth until they reached, respectively, a percentage of 73.7, 3.1 and 18.0%. These percentages would represent the optimal proportion of biochemical components in sardine early larvae and they are the result of the trade-off between, in the short term, the protein proportion necessary to optimize larval movement and growth and, in the long term, the minimum lipid percentage necessary to guarantee energy reserves to fuel metamorphosis. RNA/DNA ratio increases during larval growth up to an asymptotic optimal value of ≈3.5 in postflexion larvae. Nutritional condition of sardine larvae was good and was influenced by the parental effect through the egg biochemical composition and by the growth trajectory determined by the actual environmental conditions.     

Climate change threatens polar bear populations: a stochastic demographic analysis

The polar bear (Ursus maritimus) depends on sea ice for feeding, breeding, and movement. Significant reductions in Arctic sea ice are forecast to continue because of climate warming. We evaluated the impacts of climate change on polar bears in the southern Beaufort Sea by means of a demographic analysis, combining deterministic, stochastic, environment-dependent matrix population models with forecasts of future sea ice conditions from IPCC general circulation models (GCMs). The matrix population models classified individuals by age and breeding status; mothers and dependent cubs were treated as units. Parameter estimates were obtained from a capture-recapture study conducted from 2001 to 2006. Candidate statistical models allowed vital rates to vary with time and as functions of a sea ice covariate. Model averaging was used to produce the vital rate estimates, and a parametric bootstrap procedure was used to quantify model selection and parameter estimation uncertainty. Deterministic models projected population growth in years with more extensive ice coverage (2001-2003) and population decline in years with less ice coverage (2004-2005). LTRE (life table response experiment) analysis showed that the reduction in lambda in years with low sea ice was due primarily to reduced adult female survival, and secondarily to reduced breeding. A stochastic model with two environmental states, good and poor sea ice conditions, projected a declining stochastic growth rate, log lambdas, as the frequency of poor ice years increased. The observed frequency of poor ice years since 1979 would imply log lambdas approximately - 0.01, which agrees with available (albeit crude) observations of population size. The stochastic model was linked to a set of 10 GCMs compiled by the IPCC; the models were chosen for their ability to reproduce historical observations of sea ice and were forced with "business as usual" (A1B) greenhouse gas emissions. The resulting stochastic population projections showed drastic declines in the polar bear population by the end of the 21st century. These projections were instrumental in the decision to list the polar bear as a threatened species under the U.S. Endangered Species Act.     

Increased plant size in exotic populations: a common-garden test with 14 invasive species

The "evolution of increased competitive ability" (EICA) hypothesis predicts that exotic species will adapt to reduced herbivore pressure by losing costly defenses in favor of competitive ability. Previous studies often support the prediction that plants from exotic populations will be less well defended than plants from native populations. However, results are mixed with respect to the question of whether plants from exotic populations have become more competitive. In a common-garden experiment involving plants from two native and two exotic populations of 14 different invasive species, we tested whether exotic plants generally grow larger than conspecific native plants, and whether patterns of relative growth depend on the intensity of competition. We found a quite consistent pattern of larger exotic than native plants, but only in the absence of competition. These results suggest that invasive species may often evolve increased growth, and that increased growth may facilitate adaptation to noncompetitive environments.