bluuebunny/crossref_metadata_2025 huggingface dataset:
Consequences of heterogeneity in survival probability in a population of Florida scrub‐jays
Authors: FOX GORDON A. , KENDALL BRUCE E. , FITZPATRICK JOHN W. , WOOLFENDEN GLEN E.
Published: June 2006

Using data on breeding birds from a 35‐year study of Florida scrub‐jays Aphelocoma coerulescens (Bosc 1795), we show that survival probabilities are structured by age, birth cohort, and maternal family, but not by sex. Using both accelerated failure time (AFT) and Cox proportional hazard models, the data are best described by models incorporating variation among birth cohorts and greater mortality hazard with increasing age. AFT models using Weibull distributions with the shape parameter > 1 were always the best‐fitting models.

Shared frailty models allowing for family structure greatly reduce model deviance. The best‐fitting models included a term for frailty shared by maternal families.

To ask how long a data set must be to reach qualitatively the same conclusions, we repeated the analyses for all possible truncated data sets of 2 years in length or greater. Length of the data set affects the parameter estimates, but not the qualitative conclusions. In all but three of 337 truncated data sets the best‐fitting models pointed to same conclusions as the full data set. Shared frailty models appear to be quite robust.

The data are not adequate for testing hypotheses as to whether variation in frailty is heritable.

Substantial structured heterogeneity for survival exists in this population. Such structured heterogeneity has been shown to have substantial effects in reducing demographic stochasticity.
Census error and the detection of density dependence
Authors: FRECKLETON ROBERT P. , WATKINSON ANDREW R. , GREEN RHYS E. , SUTHERLAND WILLIAM J.
Published: June 2006

Studies aiming to identify the prevalence and nature of density dependence in ecological populations have often used statistical analysis of ecological time‐series of population counts. Such time‐series are also being used increasingly to parameterize models that may be used in population management.

If time‐series contain measurement errors, tests that rely on detecting a negative relationship between log population change and population size are biased and prone to spuriously detecting density dependence (Type I error). This is because the measurement error in density for a given year appears in the corresponding change in population density, with equal magnitude but opposite sign.

This effect introduces bias that may invalidate comparisons of ecological data with density‐independent time‐series. Unless census error can be accounted for, time‐series may appear to show strongly density‐dependent dynamics, even though the density‐dependent signal may in reality be weak or absent.

We distinguish two forms of census error, both of which have serious consequences for detecting density dependence.

First, estimates of population density are based rarely on exact counts, but on samples. Hence there exists sampling error, with the level of error depending on the method employed and the number of replicates on which the population estimate is based.

Secondly, the group of organisms measured is often not a truly self‐contained population, but part of a wider ecological population, defined in terms of location or behaviour. Consequently, the subpopulation studied may effectively be a sample of the population and spurious density dependence may be detected in the dynamics of a single subpopulation. In this case, density dependence is detected erroneously, even if numbers within the subpopulation are censused without sampling error.

In order to illustrate how process variation and measurement error may be distinguished we review data sets (counts of numbers of birds by single observers) for which both census error and long‐term variance in population density can be estimated.

Tests for density dependence need to obviate the problem that measured population sizes are typically estimates rather than exact counts. It is possible that in some cases it may be possible to test for density dependence in the presence of unknown levels of census error, for example by uncovering nonlinearities in the density response. However, it seems likely that these may lack power compared with analyses that are able to explicitly include census error and we review some recently developed methods.
The paradoxical effects of nutrient ratios and supply rates on an outbreaking insect herbivore, the Australian plague locust
Authors: CLISSOLD F. J. , SANSON G. D. , READ J.
Published: June 2006

The Australian plague locust, Chortoicetes terminifera, develops following rainfall in an environment dominated by two host plants, the annual Dactyloctenium radulans and the perennial Astrebla lappacea. This simple system provides an ideal opportunity to explore the relationship between plant quality, individual herbivore performance and population responses.

We compared the two grasses chemically and structurally, and the behavioural, physiological and developmental responses of locust nymphs to these diets.

The grasses appeared to be of similar nutritional quality in terms of their chemical composition, although they differed in their physical properties. Early instar nymphs performed equally well on both grasses. However, older nymphs consuming D. radulans developed faster, survived better and attained a higher body weight compared with those consuming A. lappacea.

The differences in performance by the older nymphs related to the rate and ratio of supply of carbohydrate and protein from the two grasses, with less carbohydrate being assimilated from A. lappacea than D. radulans per unit of protein assimilated. Experiments showed that these differences arose as a direct result of the physical barrier to nutrient extraction provided by cell walls and indirectly through the amount of water contained within each cell. Paradoxically, nitrogen did not limit performance in the traditional sense through shortage, but rather its relative excess in A. lappacea appeared to impede intake and assimilation of adequate carbohydrate.

As a consequence, we predict that the length of time D. radulans remains available following rainfall will influence plaguing dynamics, although not for the reasons previously thought.

The results highlight the need to consider nutrient balance and actual rates of supply (rather than simply measuring the chemical composition of the plant) when attempting to understand herbivore nutritional ecology.
Species richness and allometric scaling jointly determine biomass in model aquatic food webs
Authors: LONG ZACHARY T. , STEINER CHRISTOPHER F. , KRUMINS JENNIFER ADAMS , MORIN PETER J.
Published: June 2006

Allometric theory makes specific predictions about how density, and consequently biomass, scale with organism size within trophic levels, across trophic levels and across food webs.

Diversity–yield relationships suggest that more diverse food webs can sometimes support more biomass through mechanisms involving niche complementarity or selection effects that are sometimes attributed to organism size.

We combine the above two approaches and show that, generally, density and biomass scale with organism size within and between trophic levels as predicted by allometric theory. Further, food webs converged in total biomass despite persistent differences in the composition and size of the organisms among food webs; species richness explained deviations from the constant yield of biomass expected from size–abundance relationships.

Our results suggest that organism size plays only a transient role in controlling community biomass because population increases or decreases lead to rapid convergence in biomass. Species richness affects community biomass independently by effectively increasing the mass of organisms that can be supported in a given productivity regime.
Testing mechanisms of coexistence among two species of frugivorous primates
Authors: HOULE ALAIN , VICKERY WILLIAM L. , CHAPMAN COLIN A.
Published: June 2006

We examined mechanisms of coexistence between two congeneric species of frugivorous primates, the blue monkey (Cercopithecus mitis) and the red‐tailed monkey (C. ascanius).

We used giving‐up densities (the amount of food which animals leave in a patch) in fruit trees to measure foraging efficiency and to evaluate possible mechanisms of coexistence. Animals with higher giving‐up densities are less likely to persist in the company of those with lower giving‐up densities because the former are not able to exploit food patches used previously by the latter. We climbed trees to estimate giving‐up densities by counting the fruit which primates left behind.

We tested five possible mechanisms of coexistence. Three mechanisms proposed that each frugivorous species has a lower giving‐up density than the other in at least one of the following: (1) different tree species, (2) within‐tree foraging zones or (3) seasons. The fourth mechanism predicted that the socially dominant species exploits resources first and that the subordinate species has lower giving‐up densities. The final mechanism predicted that one species would find resources more quickly than the other, which would in turn have a lower giving‐up density.

Four of the five mechanisms received no support from our data. Only a trade‐off between interspecific dominance and giving‐up densities was supported.

We discuss the generality of our results and possible interactions with other factors.
Spatiotemporal stability of two beetle populations in non‐farmed habitats in an agricultural landscape
Authors: BLACKSHAW ROD P. , VERNON ROBERT S.
Published: June 2006

Understanding the spatiotemporal ecology of invertebrates in agricultural ecosystems is important for developing management strategies to enhance biodiversity and reduce pesticide use. There is increasing recognition that studies need to be undertaken at scales larger than the field but the ability to do this is often resource limited. Pheromone traps, developed for pest management, can provide a relatively cheap means of collecting data across wide geographical scales. In this study we used such traps to examine the spatial stability of two species of agrioted beetles in non‐farmed habitats over a period of 3 years.

The spatial distributions of adult male Agriotes lineatus and Agriotes obscurus were sampled from April until July at a number of sites across 950 ha on Westham Island, British Columbia, Canada. Data were assembled as spatially referenced cumulative trap counts by species and year, and analysed for evidence of aggregation and clustering using spatial analysis by distance indices (SADIE) methodology. Both intraspecific and interspecific association analyses were then carried out. A further set of analyses considered the spatial associations between different sampling dates in 2004.

Agriotes lineatus was clustered into patches and gaps at the landscape scale in all 3 years, and A. obscurus showed similar spatial structure in 2002 and 2003. For both species, spatiotemporal stability at the landscape scale was evident. There was also a positive association between the two species in 2 out of the 3 years, suggesting that they were responding in a similar manner to the landscape environment.

Synthesis and applications. This study showed that there was substantial temporal stability in the spatial structures of A. lineatus and A. obscurus in non‐farmed habitats, and that the two species respond in a broadly similar way to a heterogeneous agricultural landscape. This suggests that models to predict distributions within a landscape could be developed to guide decisions about where to grow vulnerable crops. Identification of the environmental factors that differentiate between clusters and gaps in their spatial distributions may also make it possible to manipulate populations and reduce their impact as pests without recourse to insecticides. Moreover, our results extend the spatial scales over which SADIE statistics have been used, and demonstrate the usefulness of pheromone trapping as a sampling method in addressing ecological questions at a landscape scale.
Sand dynamics in coastal dune landscapes constrain diversity and life‐history characteristics of spiders
Authors: BONTE DRIES , LENS LUC , MAELFAIT JEAN‐PIERRE
Published: June 2006

In fragmented landscapes where natural disturbance acts at the local level, community composition can be altered either by ‘species‐by‐species matching’, with community‐wide character displacement, or by ‘constrained species sorting’, whereby disturbance favours species with distinct ecological traits. It is necessary to understand such species shifts when aiming to detect bottlenecks associated with changing disturbance dynamics at different spatial levels. Such an understanding also provides insight into the underlying ecological mechanisms in operation and allows identification of species of conservation concern.

This approach to understanding species’ shifts was applied to a study of spider diversity and life‐history variation in relation to sand dynamics in stabilized and dynamic grey dune landscapes located along the coasts of France, Belgium and the Netherlands.

Local (α) diversity appeared to decrease with increasing local sand dynamics in both stable and dynamic landscapes. In dynamic dune landscapes, β‐diversity decreased significantly and approached regional (γ) diversity under local grey dune stabilization; in stabilized landscapes, β‐diversity was not affected by local sand dynamics.

Comparative analyses of ecological traits revealed shifts in life‐history patterns, suggesting that patterns in local diversity resulted from species sorting. Species from fragments characterized by high sand dynamics showed narrower niche breadths, larger body sizes and longer generation times, while summer‐active species tended to become residential after sand stabilization. This provides evidence for constrained species sorting in which natural disturbance (through local sand dynamics) allows only species with distinct ecological traits to persist.

Synthesis and applications. Species with larger body sizes, longer generation times and a higher degree of habitat specialization (i.e. related to dispersal ability) would be expected to be more vulnerable at dynamic sites and more prone to extinction than their counterparts from stabilized fragments. In particular, species with a burrowing lifestyle would be expected to go extinct locally as a result of increasing soil development and soil hardness. Shifts in species composition were found to be more pronounced in dynamic landscapes. Hence ensuring conservation of sand dynamics at a landscape level rather than at a local level is of prime importance when aiming to conserve typical psammophilous spider species within local assemblages in grey dune habitats.
The impact of variable hatching rates on parasite control: a model of an aquatic ectoparasite in a Finnish fish farm
Authors: FENTON A. , HAKALAHTI T. , BANDILLA M. , VALTONEN E. T.
Published: June 2006

Many parasites of medical and veterinary importance infect via free‐living stages that undergo a period of development in the environment before seeking a host. Frequently, considerable variation is observed in the development rates of these stages, such that some individuals may be considered to occupy distinct subpopulations, similar to a plant's seed bank. Under certain conditions, these subpopulations may act as a reservoir for the parasite, buffering it from the impact of management strategies and reducing control success.

We assessed the impact of intraspecific variation in development rates on parasite control by developing a population dynamic model of the ectoparasite Argulus coregoni, a major parasite of Finnish fish farms. We divided argulid eggs into two subpopulations: an exposed class with fast hatching rates and an ‘egg bank’ with slower hatching rates. We then assessed the success of a number of potential control strategies under a range of egg bank hatching regimes.

The predicted seasonal dynamics of the various life‐cycle stages matched well those observed in Finnish fish farms. Simulations showed that the long‐term growth rate of the argulid population tends to be reduced by the presence of a slow‐hatching egg bank, unless the egg bank affords some protection in the form of reduced egg mortality.

Sensitivity analysis showed that the key stages of the parasite's life cycle are those that relate to the on‐fish juvenile mortality and development rates. The next most sensitive parameters relate to the number of viable eggs at the start of the year, such as female fecundity and overwinter egg survival. We showed that current control approaches that target these stages could prove highly effective at suppressing the argulid population. However, long‐term control was greatly reduced in both cases as the proportion of eggs entering the egg bank increased. This was especially true if mortality of the egg bank was lower than that of the exposed eggs.

Synthesis and applications. Understanding the factors affecting parasite persistence is vital for the development of effective long‐term control. We have shown that inherent heterogeneity within a parasite population may have a substantial impact on its long‐term growth rate, and can be an important mechanism reducing the effectiveness of targeted control strategies in the field.
Land management practices for combating desertification cause species replacement of desert lizards
Authors: HAWLENA DROR , BOUSKILA AMOS
Published: June 2006

Patch structural complexity affects local species richness and population densities. Anthropogenic disturbance may alter complexity and heterogeneity, resulting in changes in community structure. Most studies in this area have dealt with human‐induced habitat degradation. We investigated a converse situation, in which anthropogenic activity increases productivity and complexity of an arid habitat.

Recently, large areas in the northern Negev Desert have been altered: a series of contour catchments was constructed to accumulate run‐off to support planted trees. We examined the effect of patch alteration by focusing on the lizard assemblage in the planted plots. Seven pairs of plots were established, one plot from each pair in a natural area and the other in an adjacent, altered slope. Lizards were captured using pitfall traps and environmental parameters were measured. To isolate the effects of trees as perches for avian predators, we ‘planted’ artificial trees in a loess plain and investigated the effect on an endemic lizard.

The structure of the lizard assemblage in the planted plots differed from that of the natural plots. Planted plots had a higher proportion of Mediterranean lizards and fewer desert species. Two local lizard species disappeared from the mosaic area of planted and natural plots. In addition, avian predators spent longer time in the artificial tree plots and reduced the lizard density compared to the natural plots.

The modification to the habitat generated only moderate changes in structure of the natural vegetation and this could not account for the observed changes in the lizard assemblage. Changes in the spatial use of the plots by avian predators was identified as the mechanism behind the observed distribution of lizard species.

Synthesis and applications. We argue that anthropogenic habitat modifications such as afforestation, urbanization, etc., can induce indirect biotic effects that may change the way and the scale at which different species respond to the habitat change. Such structural alteration may lead to species replacement and even to local extinction of specialist species. In order to protect biodiversity during large‐scale management projects, alteration of biotic interactions should be considered in advance and large unaltered patches should be protected, otherwise indirect effects might cause greater impacts than the structural manipulation itself.
Additive partitioning of diversity across hierarchical spatial scales in a forested landscape
Authors: CHANDY SHIBI , GIBSON DAVID J. , ROBERTSON PHILIP A.
Published: June 2006

Ecological phenomena exist at multiple scales, but measurements of diversity frequently consider only the smallest scale, that of the original sample plots. Additive partitioning of diversity allows multiple, hierarchical spatial scales of analysis to reveal the scale at which diversity is maximized.

We examined the spatial partitioning of diversity across 378 permanent plots established in 10 7–369‐ha research natural areas (RNA) in the 294 455‐ha Shawnee National Forest, Illinois, USA. Diversity (richness and Shannon's and Simpson's indices) was partitioned across four spatial scales, i.e. within and between plots, and between RNA and natural divisions (corresponding to α and three levels of β diversity), for two strata of vegetation (trees and woody understorey).

For both strata, the highest contribution to diversity measured as species richness was between plots and between RNA. Diversity was lower than expected within plots, although Simpson's and Shannon's indices achieved their maximum values at this scale. However, Shannon's index values were higher than Simpson's index values at the between‐RNA scale and for all strata, indicating that the most common species were found at this scale.

There was a simple asymptotic relationship between plot occupancy and local abundance, suggesting high colonization rates and rapid colonization of open habitat indicative of a wide niche breadth of the most abundant species.

Synthesis and applications.The implications of these findings are that maximum diversity across a forested landscape is not necessarily at the scale of sampling (i.e. within plots) but may be at higher scales corresponding to larger landscape units. Moreover, the largest contribution of richness to total diversity occurred at a larger scale than diversity expressed using measures based upon information theory, which incorporate species abundance and evenness. Conservation efforts seeking to preserve diversity must identify and target the correct scales to allow effective management. In this study, management at and within the RNA represents the most appropriate scale for conserving maximum diversity.
The use of image analysis to estimate population growth rate in Daphnia magna
Authors: HOOPER HELEN L. , CONNON RICHARD , CALLAGHAN AMANDA , MAUND STEVE J. , LIESS MATTHIAS , DUQUESNE SABINE , HUTCHINSON THOMAS H. , MOGGS JONATHAN , SIBLY RICHARD M.
Published: June 2006

Population growth rate (PGR) is central to the theory of population ecology and is crucial for projecting population trends in conservation biology, pest management and wildlife harvesting. Furthermore, PGR is increasingly used to assess the effects of stressors. Image analysis that can automatically count and measure photographed individuals offers a potential methodology for estimating PGR.

This study evaluated two ways in which the PGR of Daphnia magna, exposed to different stressors, can be estimated using an image analysis system. The first method estimated PGR as the ratio of counts of individuals obtained at two different times, while the second method estimated PGR as the ratio of population sizes at two different times, where size is measured by the sum of the individuals’ surface areas, i.e. total population surface area. This method is attractive if surface area is correlated with reproductive value (RV), as it is for D. magna, because of the theoretical result that PGR is the rate at which the population RV increases.

The image analysis system proved reliable and reproducible in counting populations of up to 440 individuals in 5 L of water. Image counts correlated well with manual counts but with a systematic underestimate of about 30%. This does not affect accuracy when estimating PGR as the ratio of two counts. Area estimates of PGR correlated well with count estimates, but were systematically higher, possibly reflecting their greater accuracy in the study situation.

Analysis of relevant scenarios suggested the correlation between RV and body size will generally be good for organisms in which fecundity correlates with body size. In these circumstances, area estimation of PGR is theoretically better than count estimation.

Synthesis and applications. There are both theoretical and practical advantages to area estimation of population growth rate when individuals’ reproductive values are consistently well correlated with their surface areas. Because stressors may affect both the number and quality of individuals, area estimation of population growth rate should improve the accuracy of predicting stress impacts at the population level.
Temporal and spatial development of red deer harvesting in Europe: biological and cultural factors
Authors: MILNER JOS M. , BONENFANT CHRISTOPHE , MYSTERUD ATLE , GAILLARD JEAN‐MICHEL , CSÁNYI SÁNDOR , STENSETH NILS CHR.
Published: June 2006

Deer numbers have increased dramatically throughout Europe and North America over the last century, but empirical analyses of variation in harvesting and the influence of biological and cultural factors are lacking.

We examined trends in size and composition of red deerCervus elaphusharvests over the last three to four decades in 11 European countries with contrasting deer productivity, management strategies and hunting traditions.

The harvest increased exponentially in all countries except Austria and Germany, where it was stable, and Poland, where it has declined in recent years. Harvest growth rates ranged from 0·009 in Austria to 0·075 in Sweden and depended on the management system and harvest composition, being negatively related to the proportion of females in the adult harvest.

Within four focal countries (France, Hungary, Norway and Scotland), there was considerable spatial variation in harvest growth rates. These tended to be higher in recently colonized areas than in traditional hunting areas and were often higher than the maximum possible population growth rate. Range expansion was an important component of the increase in total harvest in France and Scotland, but not in Hungary or Norway.

Harvest composition was available for seven countries, all of which showed a strong increase in the proportion of calves in the harvest. The sex ratio of the adult harvest was relatively stable, being strongly male‐biased in Norway and marginally female‐biased elsewhere. The proportion of males in the harvest was unrelated to trophy hunting objectives.

Synthesis and applications. Our study emphasizes that cultural aspects of management need to be accounted for, as well as biological factors, when interpreting the patterns of harvest growth and composition across Europe. Widespread sustained harvest growth has occurred, suggesting continued growth of deer populations with consequent social and economic impacts. Population control is therefore a major challenge for the future, currently hampered by inadequate population data and a decreasing number of hunters in some countries. Increasing the motivation of hunters to harvest female deer is one possible solution, although this may conflict with hunting traditions and economic considerations in some areas.
Genetic restoration of a stocked brown trout Salmo trutta population using microsatellite DNA analysis of historical and contemporary samples
Authors: HANSEN MICHAEL M. , BEKKEVOLD DORTE , JENSEN LASSE F. , MENSBERG KAREN‐LISE D. , NIELSEN EINAR E.
Published: June 2006

Gene flow from domesticated to wild populations is a major threat to wild salmonid fish. However, few studies have addressed how populations could be restored after admixture has occurred. We analysed the prospects for restoring the previously intensively stocked brown trout population of the Skjern River, Denmark, by identifying remaining non‐admixed individuals to be used for supportive breeding.

We analysed microsatellite DNA markers in historical (1940–50s) and contemporary (1992–2004) samples from the Skjern River system, from the strain of domesticated trout previously used for stocking, and from the neighbouring Storå River. We analysed admixture proportions to estimate the genetic contribution by domesticated trout. We identified non‐admixed trout using assignment tests, and further analysed the possible sources of indigenous trout by estimating contemporary migration among populations.

Genetic differentiation between the historical Storå and Skjern river populations was low (θST = 0·004), suggesting considerable gene flow in the past. The contemporary Skjern and Storå river populations and a supportive breeding brood stock were strongly admixed, but some non‐admixed individuals nevertheless remained in the wild‐caught samples. In addition, two resident populations in isolated tributaries were found to be indigenous. The indigenous anadromous individuals from the Skjern River were unlikely to have been recruited from either the isolated tributary populations or the neighbouring Storå River and were presumably derived from unidentified spawning sites in the river system.

All but one non‐admixed anadromous Skjern River trout were females, which we ascribed to sampling bias. Moreover, all non‐admixed fish were late‐spawning (January–February) whereas the majority of all trout caught for the study were ripe by November–December. The difference in spawning time could be an important factor delaying complete admixture of domesticated and indigenous trout.

Synthesis and applications. This study demonstrates the feasibility of restoring populations that have been admixed with exogenous individuals, by identifying non‐admixed individuals using genetic markers. However, the results also highlight the problem that numbers of identified non‐admixed individuals may be small, necessitating identification of nearby, closely related populations that can be incorporated into breeding programmes.
Altering perceived predation risk and food availability: management prescriptions to benefit farmland birds on stubble fields
Authors: WHITTINGHAM MARK J. , DEVEREUX CLAIRE L. , EVANS ANDY D. , BRADBURY RICHARD B.
Published: June 2006

European farmland bird populations have fallen dramatically and sympathetic management of key habitats is one crucial way to help boost these populations. Maximizing the value of habitats for foraging birds has largely focused on practical measures to increase food abundance, but energy intake, the key determinant of habitat quality, is also affected by food accessibility and perceived predation risk. We tested the importance of manipulating perceived predation risk and access to food on the distribution of birds on stubble fields, a key wintering habitat for many UK species and used by many species in different parts of the world.

Recent evidence suggests simple reductions in vegetation height alter perceived predation risk for some species. Light cultivation, by scarification of the soil surface, could potentially alter both perceived predation risk (via changes in vegetation structure) and food availability (by opening up the soil and bringing seeds to the surface) and so be a single solution to enhancing suitability of stubble fields for birds. In experiment 1, we investigated the effects of changing vegetation height (via topping) and scarification on vegetation structure, seed density and distribution of farmland birds, using a 2 × 2 factorial within‐field design. In experiment 2, we tested the temporal effects of scarification on bird distribution, using a similar within‐field design.

Scarified plots supported higher abundances of invertebrate feeders (e.g. thrushes). Plots that were scarified within the last 1–13 days were used more by invertebrate feeders and granivores (e.g. yellowhammer) than plots scarified 2–4 months ago. Both results were probably a consequence of food availability being temporarily increased by scarification making prey more accessible.

Granivorous passerines and invertebrate feeders preferred plots with shorter stubble while the abundance of skylarks, partridges, pigeons and meadow pipits was higher on plots with taller stubble. This was probably the result of differing anti‐predation strategies.

Synthesis and applications. Prescriptions that generate fine‐scale heterogeneity should benefit a range of species. Although our work was confined to stubble fields, the importance of simultaneous consideration of predation risk and access to food is likely to apply across European farmland landscapes and elsewhere, and could apply to other arable crops and potentially to grassland systems. On stubble fields specifically, topping of part of the field in the autumn could be combined with successive strip scarification treatments throughout the winter, to provide optimal conditions for a range of species. This could be incorporated as a management option in agri‐environment schemes such as the English Environmental Stewardship Scheme.
The ghost of past species occurrence: improving species distribution models for presence‐only data
Authors: LÜTOLF MICHAEL , KIENAST FELIX , GUISAN ANTOINE
Published: June 2006

Model‐based approaches have been used increasingly in conservation biology over recent years. Species presence data used for predictive species distribution modelling are abundant in natural history collections, whereas reliable absence data are sparse, most notably for vagrant species such as butterflies and snakes. As predictive methods such as generalized linear models (GLM) require absence data, various strategies have been proposed to select pseudo‐absence data. However, only a few studies exist that compare different approaches to generating these pseudo‐absence data.

Natural history collection data are usually available for long periods of time (decades or even centuries), thus allowing historical considerations. However, this historical dimension has rarely been assessed in studies of species distribution, although there is great potential for understanding current patterns, i.e. the past is the key to the present.

We used GLM to model the distributions of three ‘target’ butterfly species, Melitaea didyma, Coenonympha tullia and Maculinea teleius, in Switzerland. We developed and compared four strategies for defining pools of pseudo‐absence data and applied them to natural history collection data from the last 10, 30 and 100 years. Pools included: (i) sites without target species records; (ii) sites where butterfly species other than the target species were present; (iii) sites without butterfly species but with habitat characteristics similar to those required by the target species; and (iv) a combination of the second and third strategies. Models were evaluated and compared by the total deviance explained, the maximized Kappa and the area under the curve (AUC).

Among the four strategies, model performance was best for strategy 3. Contrary to expectations, strategy 2 resulted in even lower model performance compared with models with pseudo‐absence data simulated totally at random (strategy 1).

Independent of the strategy model, performance was enhanced when sites with historical species presence data were not considered as pseudo‐absence data. Therefore, the combination of strategy 3 with species records from the last 100 years achieved the highest model performance.

Synthesis and applications. The protection of suitable habitat for species survival or reintroduction in rapidly changing landscapes is a high priority among conservationists. Model‐based approaches offer planning authorities the possibility of delimiting priority areas for species detection or habitat protection. The performance of these models can be enhanced by fitting them with pseudo‐absence data relying on large archives of natural history collection species presence data rather than using randomly sampled pseudo‐absence data.
Seasonal migration of thornback rays and implications for closure management
Authors: HUNTER EWAN , BERRY FIONA , BUCKLEY AINSLEY A. , STEWART CHRISTIE , METCALFE JULIAN D.
Published: June 2006

Sharks and rays are vulnerable to fisheries exploitation because of late maturation and low fecundity, highlighting the need for effective conservation strategies. Area closures have been proposed as an appropriate management option for thornback rays in the southern North Sea, where they appear to form local subpopulations between which there is limited mixing.

To gain a fishery‐independent estimation of stock distribution, 197 thornback rays Raja clavata tagged with electronic data storage tags (DST) were released in the Thames Estuary in 1999 and 2000.

The tidal location method was used to estimate the positions of individual fish between time of release and recapture. The fishery‐independent seasonal stock distributions were integrated with landings data and a simple model was developed to estimate monthly fishing effort per International Council for the Exploration of the Sea (ICES) rectangle by different fleets and gear types.

The potential impacts of closed area management, in terms of reducing thornback ray mortality in the southern North Sea, were calculated. Spatial closures were applied either (i) as permanent closures of individual ICES rectangles or (ii) seasonally, at the level of the Thames Estuary. Catch reductions were calculated allowing for the redistribution of fishing effort.

The results confirmed the importance of the Thames Estuary for thornback rays. However, 77% of rays moved outside the estuary over winter, with seasonal migration into the Thames to spawn between March and August.

The effects of closures varied between areas and gear types. Permanent closures of individual ICES rectangles were less effective at reducing fishing mortality on rays than a spring or summer closure of the Thames Estuary as a whole, which would have a major impact on the commercially more valuable sole fishery.

Synthesis and applications. The results presented illustrate the potential impacts of a range of closure scenarios, prior to their implementation, as a basis for advice on sustainable exploitation of thornback rays. These models could be further refined by additional studies of juvenile behaviour and of other ray subpopulations in the southern North Sea.
Decline in alkali meadow vegetation cover in California: the effects of groundwater extraction and drought
Authors: ELMORE ANDREW J. , MANNING SARA J. , MUSTARD JOHN F. , CRAINE JOSEPH M.
Published: June 2006

Throughout arid regions of the world, groundwater is extracted for human population centres. In the Great Basin and Range region of the USA, we lack basic information regarding some plant communities detailing the extent to which vegetation is threatened by groundwater extraction. This is particularly true for alkali meadow vegetation, which is restricted to zones of shallow groundwater yet is not a riparian plant community with obligate wetland properties.

To increase our understanding of the relative importance of groundwater and precipitation in maintaining alkali meadow vegetation cover, we used a 16‐year record of plant cover derived from satellite data of Owens Valley, California, USA, in conjunction with concurrent depth‐to‐water and precipitation measurements, to analyse vegetation response to anthropogenic and climatic changes in water availability.

Groundwater decline varied from 0·5 to 5·0 m throughout the study area, with the largest changes occurring at sites closest to pumping wells. The entire region experienced a 6‐year drought (1987–92), during which annual precipitation remained below the 50‐year median.

Meadow plant cover over the 16‐year study period was correlated with groundwater depth, but plant cover was generally unresponsive to annual precipitation variability. Sensitivity to groundwater decline was greatest for plots with a higher cover of herbaceous perennials.

The results showed that this plant community is groundwater dependent, and that this characteristic buffers the system from the effects of drought. However, at sites with extensive groundwater decline, the remaining plant cover became weakly correlated with precipitation only after groundwater declined below a threshold depth located at 2·5 m, representing the average plant rooting depth.

Synthesis and applications. Sustainable water development that seeks to pump groundwater without adversely affecting vegetation cover and plant assemblages must recognize the maximum rooting depth of groundwater‐dependent plant species. When groundwater is within the root zone, management decisions can be made to either increase or decrease vegetation cover through modification of groundwater depth. When groundwater is below the root zone, vegetation cover is low and susceptible to changes in precipitation. Quantitative satellite measurements of vegetation cover might aid the monitoring and sustainable management of water resources.
Chloroplast microsatellites reveal colonization and metapopulation dynamics in the Canary Island pine
Authors: NAVASCUÉS MIGUEL , VAXEVANIDOU ZAFEIRO , GONZÁLEZ‐MARTÍNEZ SANTIAGO C. , CLIMENT JOSÉ. , GIL LUIS , EMERSON BRENT C.
Published: June 2006

Chloroplast microsatellites are becoming increasingly popular markers for population genetic studies in plants, but there has been little focus on their potential for demographic inference. In this work the utility of chloroplast microsatellites for the study of population expansions was explored. First, we investigated the power of mismatch distribution analysis and the FS test with coalescent simulations of different demographic scenarios. We then applied these methods to empirical data obtained for the Canary Island pine (Pinus canariensis). The results of the simulations showed that chloroplast microsatellites are sensitive to sudden population growth. The power of the FS test and accuracy of demographic parameter estimates, such as the time of expansion, were reduced proportionally to the level of homoplasy within the data. The analysis of Canary Island pine chloroplast microsatellite data indicated population expansions for almost all sample localities. Demographic expansions at the island level can be explained by the colonization of the archipelago by the pine, while population expansions of different ages in different localities within an island could be the result of local extinctions and recolonization dynamics. Comparable mitochondrial DNA sequence data from a parasite of P. canariensis, the weevil Brachyderes rugatus, supports this scenario, suggesting a key role for volcanism in the evolution of pine forest communities in the Canary Islands.
Phylogeny and biogeography of Croton alabamensis (Euphorbiaceae), a rare shrub from Texas and Alabama, using DNA sequence and AFLP data
Authors: VAN EE BENJAMIN W. , JELINSKI NICOLAS , BERRY PAUL E. , HIPP ANDREW L.
Published: June 2006

Croton alabamensis (Euphorbiaceae s.s.) is a rare plant species known from several populations in Texas and Alabama that have been assigned to var. texensis and var. alabamensis, respectively. We performed maximum parsimony, maximum likelihood, and Bayesian analyses of DNA sequences from the nuclear ribosomal internal transcribed spacer (ITS) and 5.8S regions and chloroplast trnL‐trnF regions from collections of the two varieties of C. alabamensis and from outgroup taxa. C. alabamensis emerges alone on a long branch that is sister to Croton section Corylocroton and the Cuban endemic genus Moacroton. Molecular clock analysis estimates the split of C. alabamensis from its closest relatives in sect. Corylocroton at 41 million years ago, whereas the split of the two varieties of C. alabamensis occurred sometime in the Quaternary. Amplified fragment length polymorphism (AFLP) analyses were performed using two selective primer pairs on a larger sampling of accessions (22 from Texas, 17 from Alabama) to further discriminate phylogenetic structure and quantify genetic diversity. Using both neighbour joining and minimum evolution, the populations from the Cahaba and Black Warrior watersheds in Alabama form two well‐separated groups, and in Texas, geographically distinct populations are recovered from Fort Hood, Balcones Canyonlands, and Pace Bend Park. Most of the molecular variance is accounted for by variance within populations. Approximately equal variance is found among populations within states and between states (varieties). Genetic distance between the Texas populations is significantly less than genetic distance between the Alabama populations. Both sequence and AFLP data support the same relationships between the varieties of C. alabamensis and their outgroup, while the AFLP data provide better resolution among the different geographical regions where C. alabamensis occurs. The conservation implications of these findings are discussed.
Comparison of gene expression in segregating families identifies genes and genomic regions involved in a novel adaptation, zinc hyperaccumulation
Authors: FILATOV VICTOR , DOWDLE JOHN , SMIRNOFF NICHOLAS , FORD‐LLOYD BRIAN , NEWBURY H. JOHN , MACNAIR MARK R.
Published: June 2006

One of the challenges of comparative genomics is to identify specific genetic changes associated with the evolution of a novel adaptation or trait. We need to be able to disassociate the genes involved with a particular character from all the other genetic changes that take place as lineages diverge. Here we show that by comparing the transcriptional profile of segregating families with that of parent species differing in a novel trait, it is possible to narrow down substantially the list of potential target genes. In addition, by assuming synteny with a related model organism for which the complete genome sequence is available, it is possible to use the cosegregation of markers differing in transcription level to identify regions of the genome which probably contain quantitative trait loci (QTLs) for the character. This novel combination of genomics and classical genetics provides a very powerful tool to identify candidate genes. We use this methodology to investigate zinc hyperaccumulation in Arabidopsis halleri, the sister species to the model plant, Arabidopsis thaliana. We compare the transcriptional profile of A. halleri with that of its sister nonaccumulator species, Arabidopsis petraea, and between accumulator and nonaccumulator F3s derived from the cross between the two species. We identify eight genes which consistently show greater expression in accumulator phenotypes in both roots and shoots, including two metal transporter genes (NRAMP3 and ZIP6), and cytoplasmic aconitase, a gene involved in iron homeostasis in mammals. We also show that there appear to be two QTLs for zinc accumulation, on chromosomes 3 and 7.
Evolution of Mesobuthus gibbosus (Brullé, 1832) (Scorpiones: Buthidae) in the northeastern Mediterranean region
Authors: PARMAKELIS A. , STATHI I. , CHATZAKI M. , SIMAIAKIS S. , SPANOS L. , LOUIS C. , MYLONAS M.
Published: June 2006

Sequence data derived from two mitochondrial markers, 16S rRNA and COI genes, were used to infer the evolutionary history of 47 insular and mainland populations covering most of the distributional range of the northeastern Mediterranean scorpion species Mesobuthus gibbosus. Based on the estimated divergence times of Mesobuthus lineages, the temporal frame of the genus differentiation in the northeastern Mediterranean region is placed in middle Miocene (15 million years ago). The biogeographic affinities of M. gibbosus populations point towards a mainly vicariant pattern of differentiation of the species which is consistent with the geological events that transformed the Aegean region during the period from 12 to 5 million years ago. M. gibbosus is an old northeastern Mediterranean species that has retained valuable bits of genetic information, reflecting some of the oldest vicariant events that have occurred in the area. Most importantly, the history witnessed by M. gibbosus has not been obscured by more recent palaeoevents of the region. Therefore, the case of M. gibbosus is in favour of a taxon‐oriented ‘perception’ of the natural history of a given area.