The role of local populations within a landscape context: defining and classifying sources and sinks

The interaction of local populations has been the focus of an increasing number of studies in the past 30 years. The study of source-sink dynamics has especially generated much interest. Many of the criteria used to distinguish sources and sinks incorporate the process of apparent survival (i.e., the combined probability of true survival and site fidelity) but not emigration. These criteria implicitly treat emigration as mortality, thus biasing the classification of sources and sinks in a manner that could lead to flawed habitat management. Some of the same criteria require rather restrictive assumptions about population equilibrium that, when violated, can also generate misleading inference. Here, we expand on a criterion (denoted "contribution" or Cr) that incorporates successful emigration in differentiating sources and sinks and that makes no restrictive assumptions about dispersal or equilibrium processes in populations of interest. The metric Cr is rooted in the theory of matrix population models, yet it also contains clearly specified parameters that have been estimated in previous empirical research. We suggest that estimates of emigration are important for delineating sources and sinks and, more generally, for evaluating how local populations interact to generate overall system dynamics. This suggestion has direct implications for issues such as species conservation and habitat management.     

Assessment of grazing by the freshwater copepod Diaptomus minutus using carotenoid pigments: a caution

In order to assess feeding selectivity in freshwater zooplankton, we conducted feeding trials using Diaptomus minutus isolated from two Wisconsin lakes. Copepods were fed an algal assemblage comprised of an equal biomass of a centric diatom, a cryptomonad and a coccal green alga. The total amounts of photopigments were tracked using high-performance liquid chromatography. The removals of carotenoids and a-type phorbins (chlorophyll a and phaeopigments) from feeding suspensions were compared with their presence in the guts of animals, in fecal pellets, and in the final suspension. Diaptomus minutus generally removed either the diatoms primarily or all three algal cells equally. These removals were not reflected in gut extracts of the animals, however, where alloxanthin (marker of cryptomonads) was always present, but where fucoxanthin and diadinoxanthin (markers of diatoms) were never observed. Pigment disappearance was variable for total a-type phorbins, but frequently >90% for carotenoids, particularly for fucoxanthin and diadinoxanthin. Phaeophytin a was the major a-type phorbin detected after gut passage. Our results indicate that evaluations of zooplankton grazing which assume that algal carotenoids remain detectable throughout gut passage must be made with substantial caution and that differences in pigment processing are likely to occur among zooplankton species. Furthermore, grazing experiments designed to evaluate decreases of specific pigments in feeding suspension, rather than their appearance in animals' guts, may prove a more valuable approach to understanding the feeding selectivity of copepods.      

The relative contribution of local habitat and landscape context to metapopulation processes: a dynamic occupancy modeling approach

Changes in site occupancy across habitat patches have often been attributed to landscape features in fragmented systems, particularly when considering metapopulations. However, failure to include habitat quality of individual patches can mask the relative importance of local scale features in determining distributional changes. We employed dynamic occupancy modeling to compare the strength of local habitat variables and metrics of landscape patterns as drivers of metapopulation dynamics for a vulnerable, high‐elevation species in a naturally fragmented landscape. Repeat surveys of Bicknell's thrush Catharus bicknelli presence/non‐detection were conducted at 88 sites across Vermont, USA in 2006 and 2007. We used an organism‐based approach, such that at each site we measured important local‐scale habitat characteristics and quantified landscape‐scale features using a predictive habitat model for this species. We performed a principal component analysis on both the local and landscape features to reduce dimensionality. We estimated site occupancy, colonization, and extinction probabilities while accounting for imperfect detection. Univariate, additive, and interaction models of local habitat and landscape context were ranked using AICc scores. Both local and landscape scales were important in determining changes in occupancy patterns. An interaction between scales was detected for occupancy dynamics indicating that the relationship of the parameters to local‐scale habitat conditions can change depending on the landscape context and vice versa. An increase in both landscape‐ and local‐scale habitat quality increased occupancy and colonization probability while decreasing extinction risk. Colonization and extinction were both more strongly influenced by local habitat quality relative to landscape patterns. We also identified clear, qualitative thresholds for landscape‐scale features. Conservation of large habitat patches in high‐cover landscapes will help ensure persistence of Bicknell's thrushes, but only if local scale habitat quality is maintained. Our results highlight the importance of incorporating information beyond landscape characteristics when investigating patch occupancy patterns in metapopulations.     

Assessing the impact of local habitat variables and landscape context on riparian birds in agricultural,urbanized, and native landscapes

Large tracts of natural habitat are being replaced by agriculture and urban sprawl in Mediterranean regions worldwide. We have limited knowledge about the effects of human activities on native species in these landscapes and which, if any, management practices might enhance the conservation of native biodiversity within them. Through a citizen volunteer bird-monitoring project, we compared bird abundance and species richness in northern Californian riparian zones surrounded by vineyards, urban areas, and natural areas. We assessed both local and landscape-level variables that may enhance native bird diversity in each land use type. We also demonstrate a new statistical approach, generalized estimating equations, to analyze highly variable data, such as that collected by volunteers. Avian abundance was highly correlated with both landscape context and local habitat variables, while avian richness was correlated with local habitat variables, specifically shrub richness, and percent of tree cover. In particular, shrub species richness has a strong positive correlation with riparian-preferring bird species. This suggests that active local management of riparian zones in human-dominated landscapes can increase our ability to retain native bird species in these areas.     

The relative effects of local management and landscape context on weed seed predation and carabid functional groups

Farmland biodiversity and its associated ecosystem services are affected by agricultural activities at multiple spatial scales. Among these services, the regulation of weeds by invertebrate seed predators has received much attention recently but little is known about the relative effect of local management and landscape context of fields on this process. We monitored seed predation on four common weed species and carabid communities in 28 winter-cereals fields during five consecutive weeks in spring 2010. These fields were situated in contrasted landscape contexts and varied in terms of intensity of pesticide treatments and soil tillage regimes. Weed seed predation was strongly and positively related to the Shannon diversity of (strictly) granivorous carabids and to the activity–density of omnivorous carabids but negatively to the richness of omnivorous carabids. Weed seed predation and granivore diversity were positively related to landscape diversity and the proportion cover of temporary grassland within a 1000 m radius around focal fields and were negatively affected by the intensity of local pesticide treatments. No-till systems sheltered higher diversity of granivorous carabids but did not show higher seed predation rates. We showed that landscape composition factors had a higher relative influence than local practices factors on weed seed predation service. Consequently, weed management strategies should not only consider the management of single fields but also the surrounding landscape to preserve carabid biodiversity and enhance weed seed predation service.     

Crassulacean acid metabolism in the context of other carbon-concentrating mechanisms in freshwater plants: a review

Inorganic carbon can be in short supply in freshwater relative to that needed by freshwater plants for photosynthesis because of a large external transport limitation coupled with frequent depleted concentrations of CO(2) and elevated concentrations of O(2). Freshwater plants have evolved a host of avoidance, exploitation and amelioration strategies to cope with the low and variable supply of inorganic carbon in water. Avoidance strategies rely on the spatial variation in CO(2) concentrations within and among lakes. Exploitation strategies involve anatomical and morphological features that take advantage of sources of CO(2) outside of the water column such as the atmosphere or sediment. Amelioration strategies involve carbon-concentrating mechanisms based on uptake of bicarbonate, which is widespread, C(4)-fixation, which is infrequent, and crassulacean acid metabolism (CAM), which is of intermediate frequency. CAM enables aquatic plants to take up inorganic carbon in the night. Furthermore, daytime inorganic carbon uptake is generally not inhibited and therefore CAM is considered to be a carbon-conserving mechanism. CAM in aquatic plants is a plastic mechanism regulated by environmental variables and is generally downregulated when inorganic carbon does not limit photosynthesis. CAM is regulated in the long term (acclimation during growth), but is also affected by environmental conditions in the short term (response on a daily basis). In aquatic plants, CAM appears to be an ecologically important mechanism for increasing inorganic carbon uptake, because the in situ contribution from CAM to the C-budget generally is high (18-55%).     

The effect of container size on the feeding rate of Heterocope septentrionalis, a freshwater predaceous copepod

The feeding rates of freshwater predaceous copepods have beenmeasured many times using enclosure experiments. Typically theseexperiments involve enclosing a known number of zooplanklonprey with a known number of predaceous copepods and determiningthe number of prey remaining after a set length of time. Variousfactors such as prey species and size have been shown to influencethe feeding rate of copepods. However, little attention hasbeen paid to the influence that container size may have on feedingrates. Using previously published data and some new data itwas found that container size has a major impact on the feedingrate of Heterocope septentrionalis, a predaceous freshwatercopepod common in North American arctic waters. In experimentswith Daphnia puiex, where container size varied from 0.3 to54 l (180 times), the measured feeding rate coefficient variedfrom –0.04 to –1.7 (42.5 times). Other prey speciesshowed similar changes, but the vulnerability of particularprey species to Heterocope predation remained consistent acrossthis range of expenmental containers. The reason for the containereffect is not known, but it is postulated that edge avoidanceby Heterocope may account for the observed change in feedingrate.     

Influence of local and landscape factors on bumblebees in semi-natural meadows: a multiple-scale study in a forested landscape

Understanding the effects of local and landscape factors on bumblebees is relevant for the conservation of this group of pollinators. Bumblebees have been well-studied in agricultural landscapes of Western Europe, Asia and North America, but few studies have been developed on bumblebees in forest-dominated landscapes of Eastern Europe. We developed this study in 22 semi-natural meadows located in a patchy forested landscape of Estonia. We investigated the influence of habitat characteristics and landscape factors (calculated at four spatial scales: 250, 500, 1,000 and 2,000 m radius) on the total species richness and abundance of bumblebees. Correlation analysis, partial least squares (PLS) and stepwise forward-selection multiple regression analysis were applied in this study. The presence of a high diversity of flowering plants in semi-natural meadows may benefit the abundance of bumblebees. At the local level, patch area and shape seem to have positive and negative influences, respectively, on bumblebee species richness. At the landscape level, human settlements with the presence of gardens may favour bumblebee richness and abundance. Also, bumblebee species may increase with a high presence of meadows in the landscape, and may decrease with high percentages of forest and young forest. Overall, forested landscapes with a strong presence of edges and a diverse matrix may support a higher species richness and abundance of bumblebees. Both local and landscape factors should be considered when designing conservation strategies and agri-environmental measures.     

The impact of snow accumulation on a heath spider community in a sub-Arctic landscape

Patterns of snow cover across the Arctic are expected to change as a result of shrub encroachment and climate change. As snow cover impacts both the subnivean environment and the date of spring melt, these changes could impact Arctic food webs by altering the phenology and survival of overwintering arthropods, such as spiders (Araneae). In this field study, we used snow fences to increase snow cover across a series of large (375 m²) heath tundra plots and examined the effects on the local spider community during the following growing season. Fences increased snow cover and delayed melt on the treatment plots, paralleling the conditions of nearby shrub sites. Frequent sampling over the season revealed that increased snow cover did not affect spider abundance across different genera nor did it affect overall community composition. Further, our snow treatment did not affect the dates when plots achieved seasonal catch milestones (25, 50, 75 % of total seasonal catch). Increased winter snow cover did, however, produce higher body masses in adults and juveniles of the dominant species Pardosa lapponica (Lycosidae), beginning immediately after snow melt until midway through the growing season. In addition, ovary/oocyte mass of mature P. lapponica females was significantly higher on treatment plots during the peak reproductive period. This is the first experimental manipulation study to report a significant effect of landscape-level changes to winter snow cover on the biomass of an Arctic macroarthropod.     

The predictive accuracy of population viability analysis: a test using data from two small mammal species in a fragmented landscape

This study examines the predictive accuracy of the population viability analysis package, ALEX (Analysis of the Likelihood of EXtinction). ALEX was used to predict the probability of patch occupancy for two species of small native Australian mammals (Antechinus agilis and Rattus fuscipes) among 13 patches of suitable habitat in a matrix of plantation pines (Pinus radiata). The study was retrospective, running each simulation from 1900 until 1997, and the model parameterised without knowledge of the 1997 observed field data of patch occupancy. Predictions were made over eight scenarios for each species, allowing for variation in the amount of dispersal between patches, level of environmental stochasticity, and size of habitat patches. Predicted occupancies were compared to the 1997 field data of patch occupancy using logistic regression, testing H _random, that there was no relationship between observed and predicted occupancy, and H _perfect, that there was a perfect, 1:1 relationship between observed and predicted occupancies. Rejection of H _random and failure to reject H _perfect was taken as a good match between observed and predicted occupancies. Such a match was found for one scenario with R. fuscipes, and no scenarios with A. agilis. In general, patch occupancy was underestimated, with field surveys finding that 9 of the 13 patches were occupied by R. fuscipes and 10 by A. agilis. Nonetheless, PVA predictions were in the right direction, whereby patches predicted to have a high probability of occupancy were generally occupied, and vice versa. A post hoc search over additional scenarios found few scenarios with a better match than the original eight. The results of this study support the notion that PVA is best thought of as a relative, rather than absolute predictor of the consequences of management actions in threatened populations.     

Testing the impact of calibration on molecular divergence times using a fossil-rich group: the case of Nothofagus (Fagales)

Although temporal calibration is widely recognized as critical for obtaining accurate divergence-time estimates using molecular dating methods, few studies have evaluated the variation resulting from different calibration strategies. Depending on the information available, researchers have often used primary calibrations from the fossil record or secondary calibrations from previous molecular dating studies. In analyses of flowering plants, primary calibration data can be obtained from macro- and mesofossils (e.g., leaves, flowers, and fruits) or microfossils (e.g., pollen). Fossil data can vary substantially in accuracy and precision, presenting a difficult choice when selecting appropriate calibrations. Here, we test the impact of eight plausible calibration scenarios for Nothofagus (Nothofagaceae, Fagales), a plant genus with a particularly rich and well-studied fossil record. To do so, we reviewed the phylogenetic placement and geochronology of 38 fossil taxa of Nothofagus and other Fagales, and we identified minimum age constraints for up to 18 nodes of the phylogeny of Fagales. Molecular dating analyses were conducted for each scenario using maximum likelihood (RAxML + r8s) and Bayesian (BEAST) approaches on sequence data from six regions of the chloroplast and nuclear genomes. Using either ingroup or outgroup constraints, or both, led to similar age estimates, except near strongly influential calibration nodes. Using "early but risky" fossil constraints in addition to "safe but late" constraints, or using assumptions of vicariance instead of fossil constraints, led to older age estimates. In contrast, using secondary calibration points yielded drastically younger age estimates. This empirical study highlights the critical influence of calibration on molecular dating analyses. Even in a best-case situation, with many thoroughly vetted fossils available, substantial uncertainties can remain in the estimates of divergence times. For example, our estimates for the crown group age of Nothofagus varied from 13 to 113 Ma across our full range of calibration scenarios. We suggest that increased background research should be made at all stages of the calibration process to reduce errors wherever possible, from verifying the geochronological data on the fossils to critical reassessment of their phylogenetic position.     

The scale of divergence: A phylogenetic appraisal of intercontinental allopatric speciation in a passively dispersed freshwater zooplankton genus

Molecular studies have enlightened our understanding of freshwater zooplankton biogeography, yet questions remain regarding the scale and commonality of geographic speciation. Here, we present a mtDNA-based phylogenetic hypothesis for 92 Daphnia species from all seven continents, with a focus on North and South America, Europe, and Australia, and use it to explore the frequency, scale, and geographical orientation of allopatric divergence events. Allopatric speciation can conservatively account for at least 42% of cladogenetic events among the species included in our study; most of these involve intercontinental splits. Closely related species pairs are concentrated in the circumarctic region and between northern and southern continents, aligned with bird migration routes, suggesting recent dispersal. By contrast, deeper phylogenetic patterns are consistent with vicariance scenarios linked to continental fragmentation. The possible reasons for the puzzling persistence of these ancient patterns in light of the eroding force of dispersal are considered. Our results demonstrate the high frequency and complex pattern of allopatric speciation in this ancient, passively dispersed genus.     

Mechanisms of species coexistence: a field test of theoretical models using intertidal snails

Competitor coexistence is often facilitated by spatial segregation. Traditionally, spatial segregation is predicted to occur when species differ in the habitat in which they are either superior at competing for resources or less susceptible to predation. However, predictions from a behavioural model demonstrate that spatial segregation and coexistence can also occur in the absence of such interspecific trade‐offs in competitive ability and vulnerability to predation. Unlike other models of competitor coexistence this model predicts that when species rank both habitat productivity and ‘riskinesses’ similarly, but differ slightly in their habitat‐specific vulnerabilities to predators, they will tend to segregate across habitats, with the species experiencing the higher ratio of mortality risk across the habitats occurring primarily in the safer habitat. Here, we investigate the hypothesis that intraspecific trade‐offs between resource availability and mortality risk can lead to spatial segregation of competing species by (1) documenting the spatial (i.e. intertidal) distribution of two marine snails, Littorina sitkana and L. subrotundata and (2) performing field experiments to quantify growth and mortality rates of each species at ‘low’ and ‘high’ intertidal heights. Our results indicate that both species agree on the rankings of habitat riskiness and productivity, experiencing higher predation and higher growth in low‐ than in high‐intertidal habitats. However, L. sitkana and L. subrotundata experienced differences in their habitat‐specific mortality risks and growth rates. Despite both species being similarly at risk of predation in high‐intertidal habitats (where mortality was lower), L. subrotundata was subject to significantly higher mortality than L. sitkana at the low‐intertidal height. In contrast, growth rate differences between habitats were greater for L. sitkana than for L. subrotundata. Whereas both species grew at the same rate at the high‐intertidal level (where growth was lower), L. sitkana individuals grew more rapidly than L. subrotundata snails at the low‐intertidal level. As predicted by the behavioural model, the species that experienced the higher ratio of mortality across habitats (i.e. L. subrotundata) occurred exclusively in the safer, high‐intertidal habitat. Taken together, these results provide support for the hypothesis that spatial segregation, and potentially competitor coexistence, can occur in the absence of interspecific trade‐offs in resource acquisition ability or vulnerability to predation.     

The effect of migratory behaviour on genetic diversity and population divergence: a comparison of anadromous and freshwater Atlantic salmon Salmo salar

The genetic diversity of anadromous and freshwater Atlantic salmon ( Salmo salar ) populations from north-west Russia and other north European locations was compared using microsatellite variation to evaluate the importance of anadromous migration, population size and population glacial history in determining population genetic diversity and divergence. In anadromous Atlantic salmon populations, the level of genetic diversity was significantly higher and the level of population divergence was significantly lower than among the freshwater Atlantic salmon populations, even after correcting for differences in stock size. The phylogeographic origin of the populations also had a significant effect on the genetic diversity characteristics of populations: anadromous populations from the basins of the Atlantic Ocean, White Sea and Barents Sea possessed higher levels of genetic diversity than anadromous populations from the Baltic Sea basin. Among the freshwater populations, the result was the opposite: the Baltic freshwater populations were more variable. The results of this study imply that differences in the level of long-term gene flow between freshwater populations and anadromous populations have led to different levels of genetic diversity, which was also evidenced by the hierarchical analysis of molecular variance. Furthermore, the results emphasize the importance of taking the life history of a population into consideration when developing conservation strategies: due to the limited possibilities for new genetic diversity to be generated via gene flow, it is expected that freshwater Atlantic salmon populations would be more vulnerable to extinction following a population crash. Hence, high conservation status is warranted in order to ensure the long-term survival of the limited number of European populations with this life-history strategy.     

The effects of selected sampling on the transmission disequilibrium test of a quantitative trait locus

We investigate how sampling of parents or children based on their extreme phenotypic values selected from clinical databases would affect the power of identification of quantitative trait loci (QTL) by a transmission disequilibrium test (TDT). We consider three selective sampling schemes based on the selection of phenotypic values of parents or children in nuclear families: (1) two children, one of extreme value, the other random; (2) two children extremely discordant; (3) one parent of extreme value. Other family members not specified will be recruited randomly with regard to phenotypic values. Our study shows that the second sampling scheme can always enhance the power for QTL identification, sometimes dramatically so. The increase in the statistical power of the TDT is particularly dramatic when h2 at the QTL under test is small or intermediate (e.g. 0.05 or 0.10). For the other two sampling schemes, under dominant effects at the QTL, the power is always increased relative to random sampling; however, under recessive or additive genetic effects, the power gain is generally minor or even decreased a little sometimes. Allele frequencies at the QTL and the selection stringency are important for determining the effect of selective sampling on the power of QTL identification. Our study is useful as a practical guideline on how to perform the TDT efficiently in practice by taking advantage of the extensive databases accumulated that are enriched with people of extreme phenotypic values.     

The tempo of trait divergence in geographic isolation: Avian speciation across the Marañon Valley of Peru

Geographic isolation is considered essential to most speciation events, but our understanding of what controls the pace and degree of phenotypic divergence among allopatric populations remains poor. Why do some taxa exhibit phenotypic differentiation across barriers to dispersal, whereas others do not? To test factors controlling phenotypic divergence in allopatry, we employed a comparative phylogeographic approach consisting of replicates of ecologically similar Andean bird species isolated across a major biogeographic barrier, the Marañon Valley of Peru. Our study design leverages variation among codistributed taxa in their degree of plumage, morphometric, and vocal differentiation across the Marañon to examine the tempo of phenotypic evolution. We found that substantial plumage differences between populations required roughly two million years to evolve. In contrast, morphometric trait evolution showed greater idiosyncrasy and stasis. Our results demonstrate that despite a large degree of idiosyncrasy in the relationship between genetic and phenotypic divergence across taxa and environments, comparative studies within regions may reveal predictability in the pace of phenotypic divergence. Our results also suggest that social selection is important for driving differentiation of populations found in similar environments.     

The regional effects of CO2 and landscape change using a coupled plant and meteorological model

A meteorological model, the Regional Atmospheric Modelling System (RAMS), and a plant model, the General Energy and Mass Transfer Model (GEMTM), are coupled in this study. The integrated modelling system was used to investigate regional weather conditions in the central grasslands of the USA for three experimental scenarios: ? land cover is changed from current to potential vegetation; ? radiative forcing is changed from 1 × CO₂ to 2 × CO₂; and ? biological CO₂ partial pressures are doubled. Results indicate that the biological effect of enriched CO₂, and of land‐use change exhibit dominant effects on regional meteorological and biological fields, which were observed for daily to seasonal time scales and grid to regional spatial scales. Simulated radiation impacts of 2 × CO₂ were minimal, with interactive effects between the three experimental scenarios as large as the radiational impact alone. Model results highlight the importance of including 2 × CO₂ biological effects when simulating possible future changes in regional weather.