Genomic demography: a life-history analysis of transposable element evolution.

Retrotransposons are ubiquitous mobile genetic elements that have played a significant role in shaping eukaryotic genome evolution. The genome of the yeast Saccharomyces cerevisiae harbours five families of retrotransposons, Ty1-Ty5. With the publication of the S. cerevisiae genome sequence, for the first time a full genomic complement of retrotransposon sequences is available. Analysis of these sequences promises to yield insight into the nature of host--transposon coevolution. Evolutionary change in Ty elements depends on their replication and excision rates, which have been determined in the laboratory. Rates measured in the laboratory may differ from those that have operated over evolutionary time. Based on an analysis of sequence data for the Ty1, Ty2 and hybrid Ty1/2 families, we develop a novel 'genomic demography' model to estimate long-term transposition and excision rates and to estimate how long ago these elements entered the yeast genome. We find that rates of excision and transposition have averaged 7.2-8.7 x 10(-8) per generation over evolutionary time. Two separate models provide upper- and lower-bound estimates for the age of the system, suggesting that the first elements entered the genome between approximately 50 million and 250 million generations ago.     

Direct and socially-mediated effects of food availability late in life on life-history variation in a short-lived lizard

Food availability is a major environmental factor that can influence life history within and across generations through direct effects on individual quality and indirect effects on the intensity of intra- and intercohort competition. Here, we investigated in yearling and adult common lizards (Zootoca vivipara) the immediate and delayed life-history effects of a prolonged food deprivation in the laboratory. We generated groups of fully fed or food-deprived yearlings and adults at the end of one breeding season. These lizards were released in 16 outdoor enclosures together with yearlings and adults from the same food treatment and with food-deprived or fully fed juveniles, creating four types of experimental populations. Experimental populations were then monitored during 2 years, which revealed complex effects of food on life-history trajectories. Food availability had immediate direct effects on morphology and delayed direct effects on immunocompetence and female body condition at winter emergence. Also, male annual survival rate and female growth rate and body size were affected by an interaction between direct effects of food availability and indirect effects on asymmetric competition with juveniles. Reproductive outputs were insensitive to past food availability, suggesting that female common lizards do not solely rely on stored energy to fuel reproduction. Finally, food conditions had socially-mediated intergenerational effects on early growth and survival of offspring through their effects on the intensity of competition. This study highlights the importance of social interactions among cohorts for life-history trajectories and population dynamics in stage-structured populations.     

Measuring the effects of invasive species on the demography of a rare endemic plant

The impacts of invasive species are among the greatest threats to the persistence of native species and communities. Yet most work on rare plants has focused on issues such as habitat fragmentation and genetic diversity, while few studies have quantified the impacts of invasive plants on native ones or investigated the underlying mechanisms of those impacts. I used removal experiments to assess the effects of invasive grasses on the seedling and adult demography of an endangered California endemic, Oenothera deltoidesssp. howellii. Invasive plant removal significantly increased O. deltoides seedling recruitment, but had no effect on adult plants. Differences in seedling recruitment were primarily driven by greatly increased seedling emergence rates in removal plots, although there was also some evidence of higher seedling survivorship with invasives removal. Differences in habitat type strongly influenced both the effects of removal treatments and O. deltoides demography, with areas that support natural recruitment showing weaker treatment effects and higher overall recruitment, but lower adult survivorship, compared to those under restoration through planting. These results indicate that inhibition of germination due to reduced soil disturbance, rather than resource competition, appears to be the strongest impact of invasive plants on this rare endemic. Although previous work has documented the importance of changed disturbance regimes in generating invasion impacts, invader effects on rare plants are generally presumed to result from resource competition. Studies like this one highlight the need for a greater emphasis on understanding the mechanisms by which invasive plants impact native ones, and the importance of such information in designing conservation and management strategies.     

Rapid selection effects in a short-lived semelparous squid species exposed to exploitation: inferences from the optimisation of life-history functions

The short life span of cephalopods suggests a potential for high sensitivity to the artificial selective effects of human exploitation. To explore the effects of such selection life-history optimisation was applied using data for a semelparous squid, Illex argentinus with a life span of one year. Survival and fecundity functions were combined to generate a life time reproductive potential function. The maximum reproductive potential identified the optimum age for the squid to mature. In a situation of a constant mortality rate the maximum reproductive potential was achieved at an earlier age of maturation as mortality rate increased. The exact age when the optimum maturation occurs is sensitive to the rate of mortality and the form of the assumed growth curve but covers the age range when maturation is known to occur in this species. A more realistic seasonal fishing mortality function produced a more complex fitness curve with a temporally more restricted optimal age of maturity. The selection effects will be stronger in a seasonal fishery suggesting potentially very rapid evolutionary rates. Developing analyses specifically considering frequency-dependence and environmental-feedbacks will be valuable to clarify the potential of squid to show rapid evolutionary responses to selection. Strong selection for early age of maturation could affect the yield from the fishery but more importantly, could also make the migratory strategy, on which the fishery is based, an unviable option, resulting in collapse of the fishery that exploits the migratory component of the species. This revised version was published online in July 2006 with corrections to the Cover Date.     

Refining the process of agent selection through understanding plant demography and plant response to herbivory

Abstract  Understanding plant demography and plant response to herbivory is critical to the selection of effective weed biological control agents. We adopt the metaphor of 'filters' to suggest how agent prioritisation may be improved to narrow our choices down to those likely to be most effective in achieving the desired weed management outcome. Models can serve to capture our level of knowledge (or ignorance) about our study system and we illustrate how one type of modelling approach (matrix models) may be useful in identifying the weak link in a plant life cycle by using a hypothetical and an actual weed example ( Parkinsonia aculeata ). Once the vulnerable stage has been identified we propose that studying plant response to herbivory (simulated and/or actual) can help identify the guilds of herbivores to which a plant is most likely to succumb. Taking only potentially effective agents through the filter of host specificity may improve the chances of releasing safe and effective agents. The methods we outline may not always lead us definitively to the successful agent(s), but such an empirical, data-driven approach will make the basis for agent selection explicit and serve as testable hypotheses once agents are released.     

Gene flow among small populations of a self-incompatible plant: an interaction between demography and genetics

We assessed the effects of population size and genetic relatedness on rates of pollen gene flow into experimental populations of the insect-pollinated, self-incompatible plant Raphanus sativus. We created synthetic populations of sizes 2, 5, 10, and 20 with three genetic structures (full siblings, half siblings, and unrelated plants). Following pollination in a natural setting, we conducted a simple paternity exclusion analysis using the allozyme genotypes of progeny to measure apparent gene flow and Monte Carlo simulations to estimate total gene flow. Estimates of apparent pollen gene flow rates ranged from 0 to 100% and were similar in rank to estimates of total gene flow. There were significant effects of population size and relatedness on the rate of apparent gene flow, and there were significant population size by relatedness interactions. Populations of size 2 had higher gene flow rates than larger populations, gene flow being negatively associated with the level of cross-compatibility (as measured by hand pollinations). Gene flow into populations of size 2 was also negatively associated with the distance to the nearest population of size 10 or 20. These results suggest that interactions among demography (population size), genetics (cross-compatibility), and ecology (pollinator behavior) are important influences on pollen gene flow rates into small plant populations.     

Physiological effects on demography: a long-term experimental study of testosterone's effects on fitness

Understanding physiological and behavioral mechanisms underlying the diversity of observed life-history strategies is challenging because of difficulties in obtaining long-term measures of fitness and in relating fitness to these mechanisms. We evaluated effects of experimentally elevated testosterone on male fitness in a population of dark-eyed juncos studied over nine breeding seasons using a demographic modeling approach. Elevated levels of testosterone decreased survival rates but increased success of producing extra-pair offspring. Higher overall fitness for testosterone-treated males was unexpected and led us to consider indirect effects of testosterone on offspring and females. Nest success was similar for testosterone-treated and control males, but testosterone-treated males produced smaller offspring, and smaller offspring had lower postfledging survival. Older, more experienced females preferred to mate with older males and realized higher reproductive success when they did so. Treatment of young males increased their ability to attract older females yet resulted in poor reproductive performance. The higher fitness of testosterone-treated males in the absence of a comparable natural phenotype suggests that the natural phenotype may be constrained. If this phenotype were to arise, the negative social effects on offspring and mates suggest that these effects might prevent high-testosterone phenotypes from spreading in the population.     

The effects of fire frequency and grazing on tallgrass prairie productivity and plant composition are mediated through bud bank demography

Periodic fire, grazing, and a variable climate are considered the most important drivers of tallgrass prairie ecosystems, having large impacts on the component species and on ecosystem structure and function. We used long-term experiments at Konza Prairie Biological Station to explore the underlying demographic mechanisms responsible for tallgrass prairie responses to two key ecological drivers: fire and grazing. Our data indicate that belowground bud banks (populations of meristems associated with rhizomes or other perennating organs) mediate tallgrass prairie plant response. Fire and grazing altered rates of belowground bud natality, tiller emergence from the bud bank, and both short-term (fire cycle) and long-term (>15 year) changes in bud bank density. Annual burning increased grass bud banks by 25% and decreased forb bud banks by 125% compared to burning every 4 years. Grazing increased the rate of emergence from the grass bud bank resulting in increased grass stem densities while decreasing grass bud banks compared to ungrazed prairie. By contrast, grazing increased both bud and stem density of forbs in annually burned prairie but grazing had no effect on forb bud or stem density in the 4-year burn frequency treatment. Lastly, the size of the reserve grass bud bank is an excellent predictor of long-term ANPP in tallgrass prairie and also of short-term interannual variation in ANPP associated with fire cycles, supporting our hypothesis that ANPP is strongly regulated by belowground demographic processes. Meristem limitation due to management practices such as different fire frequencies or grazing regimes may constrain tallgrass prairie responses to interannual changes in resource availability. An important consequence is that grasslands with a large bud bank may be the most responsive to future climatic change or other global change phenomena such as nutrient enrichment, and may be most resistant to exotic species invasions.     

Delineating the effects of a plant trait on interactions among associated insects

Plant traits can affect ecological interactions between plants, herbivores, and predators. Our study tests whether reduced leaf wax in peas alters the interaction between the pea aphid ( Acyrthosiphon pisum), a foliar-foraging predator (a lady beetle, Hippodamia convergens) and a ground-foraging predator (a ground beetle, Poecilus scitulus). We performed a 2×2×2 factorial experiment in which wax level, presence of H. convergens, and presence of P. scitulus were manipulated. Experimental arenas consisted of a cage surrounding three pea plants. One plant in each cage was stocked with 15 pea aphids. In greenhouse and field cage experiments, we assessed the effect of each factor and their interactions on aphid density. As in previous studies, H. convergens foraged for aphids more effectively on reduced wax peas than on normal peas. Other interactions among H. convergens, P. scitulus , and A. pisum were the same on both types of peas. We consider how aphid movement, plant growth, and a high frequency of predation by P. scitulus on H. convergens influenced pea aphid density.     

Predation effects on the evolution of life-history traits in a clonal oligochaete

Although size at maturity and size and number of offspring are life-history traits widely studied in sexual and parthenogenetic reproduction, there is no such research on animals reproducing asexually without the involvement of gametes. Here we present an individual-based model in combination with experiments to study the clonal growth of Stylaria lacustris, an oligochaete reproducing through fission. We studied the effect of individual size at fission and fission ratio on clone fitness. Our results show that in benign environments without predators, fitness is higher when small worms produce small offspring. Then we included size-specific sublethal predation and found that the fitness of the clone is maximized when parental worms start fission at a large size and produce large descendants intercalated in the middle of the parental worm's body. These results agree with empirical findings. Furthermore, the results of our own laboratory experiment revealed that when S. lacustris is exposed to chemical alarm signals from injured conspecifics, it alters its life history in the same direction as predicted by the model. Our findings suggest that the effect of size-specific sublethal predation is similar to the effect of size-specific lethal predation because both modes of predation result in size-dependent prey mortality.     

Chemical defence in a sawfly: genetic components of variation in relevant life-history traits

Larvae of several tenthredinid sawfly species readily release droplets of haemolymph through their integument when attacked by predators. This defence mechanism via 'bleeding' is characterised by a low integument resistance and a high haemolymph deterrence. Both traits are variable, and negatively correlated among species. We sought to determine if such differences in the propensity to bleed also occur intraspecifically by studying the heritability of traits potentially associated with the bleeding phenomenon in the turnip sawfly Athalia rosae ruficornis Jakovlev (Hymenoptera: Tenthredinidae, Allantinae). For three European populations, heritabilities were estimated in the laboratory in a parent-offspring and a full-sib design for haemolymph deterrence (measured as concentration of sequestered glucosinolate), integument resistance, body mass of eonymph and adult, and developmental time. Within A. rosae, no significant negative phenotypic correlation was found between the two traits directly related to the defence mechanism: integument resistance and haemolymph deterrence. However, the significant heritabilities found for these traits in the full-sib analysis (0.39 and 0.35, respectively, for males in the Swiss population) show that the variation has a genetic component. While full-sib analysis revealed highly significant heritabilities for most traits in all the three populations, parent-offspring regression revealed little or no evidence of heritable variation. Effects of common environment for siblings and variation in the host-plant quality between insect generations are likely to be the main factors explaining these differences. A consequence of such host-plant variation in the wild might be that genetic variation of such chemical defensive traits is largely invisible to natural selection.     

Experimental life-history evolution: selection on growth form and its plasticity in a clonal plant

The growth form along the continuum from compact phalanx plants to more loosely packed guerilla plants is an important life-history trait in clonal plants. Prerequisite for its evolution is heritable genetic variation. Starting with 102 genotypes of the stoloniferous herb Ranunculus reptans, we performed one selection experiment on spatial spread per rosette as measure of guerillaness (broad-sense heritability 0.198) and another on plasticity in this trait in response to competition (broad-sense heritability 0.067). After two generations, spatial spread was 36.9% higher in the high line than in the low line (realized heritability +/- SE 0.149 +/- 0.039). Moreover, compared with the low line genotypes of the high line had fewer rosettes, a lower proportion of flowering rosettes, a higher proportion of rooted rosettes, more branches per rosette, longer internodes and longer leaves. In the second experiment, we found no significant direct response to selection for high and low plasticity in spatial spread (realized heritability +/- SE -0.029 +/- 0.063), despite a significant correlated response in plasticity in the length of the first three stolon internodes. Our study indicates a high potential for further evolution of the clonal growth form in R. reptans, but not for its plasticity, and it demonstrates that the clonal growth form does not evolve independently of other clonal life-history characteristics.     

Modelling the effects of genetics and habitat on the demography of a grassland herb

There is growing evidence that genetic and ecological factors interact in determining population persistence. The demographic effects of inbreeding depression can largely depend on the ecological milieu. We used demographic data of the perennial herb Succisa pratensis from six populations in grazed and ungrazed sites with different soil moisture. We built an individual-based model assessing the demographic consequences of inbreeding depression in populations with different management and habitat. Today this plant has to cope with severe landscape fragmentation, deteriorating habitat conditions in terms of decreasing grazing intensity, and the effects of inbreeding depression. For each population we performed simulations testing two inbreeding depression hypotheses (partial dominance and overdominance) and three epistatic functions among loci. The results indicated stronger inbreeding depression effects for populations in unfavourable sites without grazing or in xeric habitats compared to populations in favourable mesic sites with grazing. Overall, we found stronger effects with overdominance, a result that emphasizes the importance of understanding the genetic mechanisms of inbreeding depression. Hence, management practices can interact with the genetic consequences of inbreeding depression in population dynamics, which may have important implications for plant population ecology and evolutionary dynamics of inbreeding depression.     

Feedback effects of chronic browsing on life-history traits of a large herbivore

1. Increasing ungulate populations are affecting vegetation negatively in many areas, but few studies have assessed the long-term effects of overbrowsing on individual life-history traits of ungulates. 2. Using an insular population of white-tailed deer (Odocoileus virginianus Zimmermann; Anticosti, Québec, Canada) introduced in 1896, and whose density has remained high since the first evidence of severe browsing in the 1930s, we investigated potential feedbacks of long-term and heavy browsing on deer life-history traits. 3. We assessed whether chronic browsing contributed to a decline of the quality of deer diet in early autumn during the last 25 years, and evaluated the impacts of reduced diet quality on deer body condition and reproduction. 4. Rumen nitrogen content declined 22% between two time periods, 1977-79 and 2002-04, indicating a reduction in diet quality. 5. After accounting for the effects of year within the time period, age and date of harvest in autumn, peak body mass of both sexes declined between the two time periods. At the end of November, males were on average 12% heavier and adult does 6% heavier in 1977-79 than in 2002-04. Hind foot length did not vary between time periods. 6. The probability of conception increased 15% between the two time periods, but litter size at ovulation declined 7%, resulting in a similar total number of ovulations in 2002-04 and in 1977-79. 7. Our results suggest that following a decline in diet quality, white-tailed deer females modified their life-history strategies to maintain reproduction at the expense of growth. 8. Deer appear to tolerate drastic reductions in diet quality by modifying their life history traits, such as body mass and reproduction, before a reduction in density is observed. Such modifications may contribute to maintain high population density of large herbivores following population irruption.     

Evidence for a shift in life-history strategy during the secondary phase of a plant invasion

We investigated the correlated response of several key traits of Lythrum salicaria L. to water availability gradients in introduced (Iowa, USA) and native (Switzerland, Europe) populations. This was done to investigate whether plants exhibit a shift in life-history strategy during expansion into more stressful habitats during the secondary phase of invasion, as has recently been hypothesized by Dietz and Edwards (Ecology 87(6):1359, 2006). Plants in invaded habitats exhibited a correlated increase in longevity and decrease in overall size in the transition into more stressful mesic habitats. In contrast, plants in the native range only exhibited a decrease in height. Our findings are consistent with the hypothesis that secondary invasion is taking place in L. salicaria, allowing it to be more successful under the more stressful mesic conditions in the invaded range. If this trend continues, L. salicaria may become a more problematic species in the future.     

Within- and between-generation effects of temperature on life-history traits in a butterfly

Non-genetic parental effects may largely affect offspring phenotype, and such plasticity is potentially adaptive. Despite its potential importance, little is known about cross-generational effects of temperature, at least partly because parental effects were frequently considered a troublesome nuisance, rather than a target of experimental studies. We here investigate effects of parental, developmental and acclimation temperature on life-history traits in the butterfly Bicyclus anynana. Higher developmental temperatures reduced development times and egg size, increased egg number, but did not affect pupal mass. Between-generation temperature effects on larval time, pupal time, larval growth rate and egg size were qualitatively very similar to effects of developmental temperature, and additionally affected pupal mass but not egg number. Parental effects are important mediators of phenotypic plasticity in B. anynana, and partly yielded antagonistic effects on different components of fitness, which may constrain the evolution of cross-generational adaptive plasticity.     

Survival costs of reproduction in a short-lived perennial plant: Live hard, die young

According to life-history theory, reproductive investments involve costs in terms of growth, future fecundity, and/or survival. However, studies to date have often failed to detect costs of reproduction, with survival costs among the less documented. We investigated the cost of reproduction in Helianthemum squamatum (Cistaceae), a short-lived perennial of semiarid Mediterranean environments. After experimental flower removal, we evaluated next season's growth, reproduction, and survival of the plants. We also monitored an indicator of plant physiological status (F(v)/F(m)) and leaf nutrient concentration at key phenological stages during reproduction. Survival rate in deblossomed plants was significantly higher than in control plants. As far as we know, this is the first experimental evidence of a survival cost of reproduction in a perennial plant. In contrast, no cost to growth or reproduction was found during the next season, and no significant differences in F(v)/F(m) or leaf nutrients were found between control and deblossomed plants. Helianthemum squamatum's success in semiarid Mediterranean ecosystems seems to rely on a persistent seed bank, combined with a sustained high reproductive output at the expense of survival. We conclude that this strategy might be more common than previously thought among short-lived shrubby plants growing in stressful Mediterranean areas.