Using simulations to evaluate Mantel‐based methods for assessing landscape resistance to gene flow

Mantel‐based tests have been the primary analytical methods for understanding how landscape features influence observed spatial genetic structure. Simulation studies examining Mantel‐based approaches have highlighted major challenges associated with the use of such tests and fueled debate on when the Mantel test is appropriate for landscape genetics studies. We aim to provide some clarity in this debate using spatially explicit, individual‐based, genetic simulations to examine the effects of the following on the performance of Mantel‐based methods: (1) landscape configuration, (2) spatial genetic nonequilibrium, (3) nonlinear relationships between genetic and cost distances, and (4) correlation among cost distances derived from competing resistance models. Under most conditions, Mantel‐based methods performed poorly. Causal modeling identified the true model only 22% of the time. Using relative support and simple Mantel r values boosted performance to approximately 50%. Across all methods, performance increased when landscapes were more fragmented, spatial genetic equilibrium was reached, and the relationship between cost distance and genetic distance was linearized. Performance depended on cost distance correlations among resistance models rather than cell‐wise resistance correlations. Given these results, we suggest that the use of Mantel tests with linearized relationships is appropriate for discriminating among resistance models that have cost distance correlations <0.85 with each other for causal modeling, or <0.95 for relative support or simple Mantel r. Because most alternative parameterizations of resistance for the same landscape variable will result in highly correlated cost distances, the use of Mantel test‐based methods to fine‐tune resistance values will often not be effective.     

Dealing with uncertainty in landscape genetic resistance models: a case of three co‐occurring marsupials

Landscape genetics lacks explicit methods for dealing with the uncertainty in landscape resistance estimation, which is particularly problematic when sample sizes of individuals are small. Unless uncertainty can be quantified, valuable but small data sets may be rendered unusable for conservation purposes. We offer a method to quantify uncertainty in landscape resistance estimates using multimodel inference as an improvement over single model‐based inference. We illustrate the approach empirically using co‐occurring, woodland‐preferring Australian marsupials within a common study area: two arboreal gliders (Petaurus breviceps, and Petaurus norfolcensis) and one ground‐dwelling antechinus (Antechinus flavipes). First, we use maximum‐likelihood and a bootstrap procedure to identify the best‐supported isolation‐by‐resistance model out of 56 models defined by linear and non‐linear resistance functions. We then quantify uncertainty in resistance estimates by examining parameter selection probabilities from the bootstrapped data. The selection probabilities provide estimates of uncertainty in the parameters that drive the relationships between landscape features and resistance. We then validate our method for quantifying uncertainty using simulated genetic and landscape data showing that for most parameter combinations it provides sensible estimates of uncertainty. We conclude that small data sets can be informative in landscape genetic analyses provided uncertainty can be explicitly quantified. Being explicit about uncertainty in landscape genetic models will make results more interpretable and useful for conservation decision‐making, where dealing with uncertainty is critical.     

绵羊的采食行为与草场空间异质性关系

在中国科学院内蒙古草原生态系统定位研究站,于１９９３年６月,７月９月,分别对放牧率为４羊／ｈｍ＾２的围栏放牧草场上绵羊采集行为与草场空间异质性的关系进行了定量研究,结果表明,绵羊的采食运动模式与草场空间异质性密切相关,采食区域和卧息及反刍地点相对稳定,对草场的利用依植物群落种类组成的变化有不同的采集顺序,一般地,多选择大针茅,寸草苔,星毛萎陵菜较少的平地上采食,饮水点对采食路线和目标的选择有一定的     

Size‐structured vulnerability of the colonial cyanobacterium,Microcystis aeruginosa,to grazing by zebra mussels (Dreissena polymorpha)

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Demographic patterns of a widespread long‐lived tree are associated with rainfall and disturbances along rainfall gradients in SE Australia

Predicting species distributions with changing climate has often relied on climatic variables, but increasingly there is recognition that disturbance regimes should also be included in distribution models. We examined how changes in rainfall and disturbances along climatic gradients determined demographic patterns in a widespread and long‐lived tree species, Callitris glaucophylla in SE Australia. We examined recruitment since 1950 in relation to annual (200–600 mm) and seasonal (summer, uniform, winter) rainfall gradients, edaphic factors (topography), and disturbance regimes (vertebrate grazing [tenure and species], fire). A switch from recruitment success to failure occurred at 405 mm mean annual rainfall, coincident with a change in grazing regime. Recruitment was lowest on farms with rabbits below 405 mm rainfall (mean = 0–0.89 cohorts) and highest on less‐disturbed tenures with no rabbits above 405 mm rainfall (mean = 3.25 cohorts). Moderate levels of recruitment occurred where farms had no rabbits or less disturbed tenures had rabbits above and below 405 mm rainfall (mean = 1.71–1.77 cohorts). These results show that low annual rainfall and high levels of introduced grazing has led to aging, contracting populations, while higher annual rainfall with low levels of grazing has led to younger, expanding populations. This study demonstrates how demographic patterns vary with rainfall and spatial variations in disturbances, which are linked in complex ways to climatic gradients. Predicting changes in tree distribution with climate change requires knowledge of how rainfall and key disturbances (tenure, vertebrate grazing) will shift along climatic gradients.     

Experimental Analysis of Grazing by the Mayfly Meridialaris chiloeensis on Different Successional Stages of Stream Periphyton

In this study we determined grazing effects of the South Andean endemic mayfly Meridialaris chiloeensis on periphyton at different stages of successional development. Grazing effects were studied through a two‐factor experimental design (colonization stages X grazer density) in a stream‐side channel in spring and winter. Our results showed an absence of proportionality between grazer density and periphyton decline in response to grazers at low and intermediate levels of periphytic biomass; however, when periphyton biomass was high a direct inverse relationship was observed between post‐grazing biomass and grazer density. The relationship between periphytic algae (chlorophyll a concentration) and periphyton (total periphytic ash‐free dry mass) (C/OM index) was used as an estimation of the autotrophic fraction in the total periphyton matrix. Grazing did not alter the C/OM index indicating that both autotrophic and heterotrophic fractions of the periphyton components were reduced in the same proportion. Ordination of samples using the relative abundance of diatom species showed that herbivore effect was less evident at intermediate and late stage of colonization than at early one. These results support the statement that the outcome of the herbivore‐periphyton interaction may depend on the successional stage of the periphyton community. In spring Fragilaria pinnata relative abundance, on the basis of cell counts, was reduced by grazing and Nitzschia palea was enhanced. In the winter experiment, grazing decreased Achnanthes minutissima relative abundance. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

Discrepancies between net particulate carbon production and 13C‐labelled bicarbonate uptake by Alexandrium catenella (Dinophyceae): grazing controls the balance between autotrophic and non autotrophic carbon acquisition1

Inorganic carbon uptake by Alexandrium catenella estimated from incorporation of ¹³C labelled bicarbonate (an estimate of carbon gain by autotrophy) was compared to increases in particulate carbon (PC) that integrate all processes leading to carbon gain by cells (autotrophy, heterotrophy, mixotrophy). During blooms of A. catenella in the field, the ¹³C tracer technique could account for only 47% (range 29%–59%) of the increase in PC in conventional 24 h incubations. From dilution experiments, the ratio of PC increases to bicarbonate uptake was related significantly and positively to the grazing rate, indicating that dissolved organic carbon contributes to growth as a direct function of grazing activity. In addition, as grazing rate increases, the contribution of dissolved inorganic carbon uptake to carbon‐based growth decreases in a linear way (from 56% to 33% of total C acquisition) and the contribution of non autotrophic processes increases (from 54% to 67%). Thus, grazing appears to closely control the balance between autotrophic and non autotrophic processes leading to carbon acquisition by natural populations of A. catenella.     

Does alpine grazing reduce blazing? A landscape test of a widely‐held hypothesis

Abstract ‘Alpine grazing reduces blazing’ is a widely and strongly held view concerning the effects of livestock grazing on fuels, and therefore fire behaviour and impact, in Australia's high country landscapes. As a test of this hypothesis, we examined the patterns of burning across the alpine (treeless) landscapes of the Bogong High Plains in Victoria, following the extensive fires of January 2003. Data were collected from multiple transects, each 3–5 km long, with survey points located randomly at either 50, 200 or 500 m intervals. The transects traversed the major regions of the Bogong High Plains, both grazed and ungrazed. At each point, we recorded whether the point was burnt or unburnt, the vegetation type (closed‐heath, open‐heath, grassland or herbfield), the estimated prefire shrub cover, slope, aspect, and a GPS location. At burnt heathland sites, we recorded the minimum twig diameter (an a posteriori measure of fire severity) in a sample of common shrubs. In total, there were 108 km of transect lines, 419 survey points and 4050 twig measurements, with sample points equally distributed across grazed and ungrazed country. The occurrence of fire (i.e. burnt or unburnt) in grazed and ungrazed areas was analysed by logistic regression; the variation in twig diameters by anova . Approximately half of all points were burnt. There was no statistically significant difference between grazed and ungrazed areas in the proportion of points burnt. Fire occurrence was determined primarily by vegetation type, with the proportion burnt being 0.87 for closed‐heath, 0.59 for open‐heath, and 0.13 for grassland and all snow‐patch herbfield points unburnt. In both closed‐heath and open‐heath, grazing did not significantly lower the severity of fire, as measured by the diameter of burnt twigs. We interpret the lack of a grazing effect in terms of shrub dynamics (little or no grazing effect on long‐term cover of taller shrubs), diet and behaviour of cattle (herbs and dwarf shrubs eaten; tall shrubs not eaten and closed‐heath vegetation generally avoided), and fuel flammability (shrubs more flammable than grass). Whatever effects livestock grazing may have on vegetation cover, and therefore fuels in alpine landscapes, they are likely to be highly localized, with such effects unlikely to translate into landscape‐scale reduction of fire occurrence or severity. The use of livestock grazing in Australian alpine environments as a fire abatement practice is not justified on scientific grounds.     

Satellite observed widespread decline in Mongolian grasslands largely due to overgrazing

The Mongolian Steppe is one of the largest remaining grassland ecosystems. Recent studies have reported widespread decline of vegetation across the steppe and about 70% of this ecosystem is now considered degraded. Among the scientific community there has been an active debate about whether the observed degradation is related to climate, or over‐grazing, or both. Here, we employ a new atmospheric correction and cloud screening algorithm (MAIAC) to investigate trends in satellite observed vegetation phenology. We relate these trends to changes in climate and domestic animal populations. A series of harmonic functions is fitted to Moderate Resolution Imaging Spectroradiometer (MODIS) observed phenological curves to quantify seasonal and inter‐annual changes in vegetation. Our results show a widespread decline (of about 12% on average) in MODIS observed normalized difference vegetation index (NDVI) across the country but particularly in the transition zone between grassland and the Gobi desert, where recent decline was as much as 40% below the 2002 mean NDVI. While we found considerable regional differences in the causes of landscape degradation, about 80% of the decline in NDVI could be attributed to increase in livestock. Changes in precipitation were able to explain about 30% of degradation across the country as a whole but up to 50% in areas with denser vegetation cover (P < 0.05). Temperature changes, while significant, played only a minor role (r² = 0.10, P < 0.05). Our results suggest that the cumulative effect of overgrazing is a primary contributor to the degradation of the Mongolian steppe and is at least partially responsible for desertification reported in previous studies.     

Beyond the landscape: Resistance modelling infers physical and behavioural gene flow barriers to a mobile carnivore across a metropolitan area

Urbanization affects key aspects of wildlife ecology. Dispersal in urban wildlife species may be impacted by geographical barriers but also by a species’ inherent behavioural variability. There are no functional connectivity analyses using continuous individual‐based sampling across an urban‐rural continuum that would allow a thorough assessment of the relative importance of physical and behavioural dispersal barriers. We used 16 microsatellite loci to genotype 374 red foxes (Vulpes vulpes) from the city of Berlin and surrounding rural regions in Brandenburg in order to study genetic structure and dispersal behaviour of a mobile carnivore across the urban‐rural landscape. We assessed functional connectivity by applying an individual‐based landscape genetic optimization procedure. Three commonly used genetic distance measures yielded different model selection results, with only the results of an eigenvector‐based multivariate analysis reasonably explaining genetic differentiation patterns. Genetic clustering methods and landscape resistance modelling supported the presence of an urban population with reduced dispersal across the city border. Artificial structures (railways, motorways) served as main dispersal corridors within the cityscape, yet urban foxes avoided densely built‐up areas. We show that despite their ubiquitous presence in urban areas, their mobility and behavioural plasticity, foxes were affected in their dispersal by anthropogenic presence. Distinguishing between man‐made structures and sites of human activity, rather than between natural and artificial structures, is thus essential for better understanding urban fox dispersal. This differentiation may also help to understand dispersal of other urban wildlife and to predict how behaviour can shape population genetic structure beyond physical barriers.     

Abiotic effects predominate under prolonged livestock‐induced disturbance

Despite the widespread recognition that disturbance by livestock affects multiple indices of landscape health, few studies have examined their effects on both biotic and abiotic processes. We examined the effects of livestock disturbance on soil, vascular plants and reptiles across a disturbance gradient in a semi‐arid Australian woodland. Our gradient ranged from long‐ungrazed water remote sites, through intermediately grazed recovering sites, to currently grazed sites close to water. Our aim was to examine the nature of the effects of grazing‐induced disturbance on biotic and abiotic processes along the gradient. We detected small biotic effects, but no abiotic effects, at low levels of disturbance (intermediate sites). We could not detect a consistent biotic effect on plants or reptiles along the gradient, except between the extreme disturbances. In contrast, we recorded substantial reductions in abiotic structure and function at the most disturbed sites. Structural changes included reductions in the cover of shrub hummocks and increases in bare soil, and reductions in cryptogamic soil crusts. Structural changes were associated with declines in function (soil stability and nutrient indices). Our data are consistent with the notion that abiotic effects predominate at high levels of disturbance in rangelands. Given the extent of abiotic modification at currently grazed sites, the cover of abiotic elements such as hummocks and soil surfaces would seem a better indicator of the long‐term effect of grazing‐induced disturbance than biotic components. The extent of disturbance at currently grazed sites across large areas of rangeland suggests that autogenic recovery will be protracted.     

Top‐down regulation of filamentous cyanobacteria varies among a raptorial versus current feeding copepod across multiple prey generations

1. Although considered a key functional trait, little is known about how zooplankton feeding mode affects top‐down regulation of phytoplankton communities. Indeed, copepods are expected to promote the dominance of toxic phytoplankton by selective removal of their edible competitors; however, empirical evidence comparing the effect among calanoid and cyclopoid copepods is lacking.
2. We compared the top‐down effects of two copepods with contrasting feeding modes—the calanoid Notodiaptomus iheringi (current feeder) and the cyclopoid Thermocyclops decipiens (ambush feeder) — on the relative and absolute biomass of the filamentous cyanobacterium Raphidiopsis raciborskii co‐cultured with the nutritious eukaryotic phytoplankton Cryptomonas obovata in a week‐long laboratory assay.
3. The current feeder had a stronger top‐down effect on the biomass of both prey throughout the experiment, with mass‐specific clearance rates 3–5× higher than ambush feeder. By the end of the experiment, the current feeder significantly reduced cyanobacteria biomass compared to controls while the ambush feeder did not. During the week‐long experiment, the current feeder switched from grazing on edible prey to cyanobacteria as the former became less abundant.
4. Contrary to expectation, neither of the copepod species promoted cyanobacterial dominance by the end of the experiment. This is because both grazers, but especially the current feeder, initially increased but subsequently decreased the relative contribution of cyanobacteria to total phytoplankton biomass. Moreover, both copepods decreased the length of cyanobacteria filaments by c. 70%
5. Current feeders can switch from edible prey to cyanobacteria when the abundance of shortened filaments surpasses the abundance of edible prey. While top‐down regulation of phytoplankton can be stronger for current feeding copepods, ambush feeding copepods can have a significant role during blooms by shortening cyanobacterial filaments. Hence, the broader role of contrasting copepod feeding traits on phytoplankton communities merits further study.

     

Rapid recovery of mammal fauna in the central Kimberley,northern Australia,following the removal of introduced herbivores

Australia has lost more native mammal species than any other country in the past two centuries, and this record of loss looks likely to worsen over the next few decades. Small‐ to medium‐sized mammals are declining in both distribution and density across large tracts of northern Australia's tropical savannas, including within protected areas. The most likely causes are a combination of changed fire patterns, the impacts of introduced herbivores and predation by feral cats. Here, in contrast to the prevailing trend across northern Australia, we report the recovery of native mammals in response to a large‐scale (>40 000 ha) destocking experiment carried out at Mornington Wildlife Sanctuary in the central Kimberley, north‐west Australia. Following the removal of introduced herbivores from 2004, the species richness and abundance of small native rodents and dasyurids increased significantly across all sampled habitats over the next 3 years. We discuss the implications of these results for guiding land management and applied research to help to reduce the impending risk of mammalian extinctions in northern Australia.     

Detection of environmental and morphological adaptation despite high landscape genetic connectivity in a pest grasshopper (Phaulacridium vittatum)

Widespread species that exhibit both high gene flow and the capacity to occupy heterogeneous environments make excellent models for examining local selection processes along environmental gradients. Here we evaluate the influence of temperature and landscape variables on genetic connectivity and signatures of local adaptation in Phaulacridium vittatum, a widespread agricultural pest grasshopper, endemic to Australia. With sampling across a 900‐km latitudinal gradient, we genotyped 185 P. vittatum from 19 sites at 11,408 single nucleotide polymorphisms (SNPs) using ddRAD sequencing. Despite high gene flow across sites (pairwise F_ST = 0.0003–0.08), landscape genetic resistance modelling identified a positive nonlinear effect of mean annual temperature on genetic connectivity. Urban areas and water bodies had a greater influence on genetic distance among sites than pasture, agricultural areas and forest. Together, F_ST outlier tests and environmental association analysis (EAA) detected 242 unique SNPs under putative selection, with the highest numbers associated with latitude, mean annual temperature and body size. A combination of landscape genetic connectivity analysis together with EAA identified mean annual temperature as a key driver of both neutral gene flow and environmental selection processes. Gene annotation of putatively adaptive SNPs matched with gene functions for olfaction, metabolic detoxification and ultraviolet light shielding. Our results imply that this widespread agricultural pest has the potential to spread and adapt under shifting temperature regimes and land cover change.     

Effects of deferring grazing on the floristic diversity of Stipa tenacissima Loefl. ex L. rangelands in central Algerian steppe

The present work aims to study the effect of deferring grazing on the floristic diversity of Stipa tenacissima Loefl. ex L. rangelands in the central Algerian steppe in two different bioclimatic stages, namely semi‐arid and arid. This work is part of a perspective to know the floristic characteristics of an area excluded from grazing and an unrestricted rangeland, in two different environments in order to highlight the factors that are conceivably responsible for the diversification of flora in the steppe ecosystems. In the present study, a number of 96 floristic surveys were performed during the spring season of the years 2014, 2015 and 2016. The methodology adopted is a subjective sampling. The minimum area retained is 100 m² defined by the method of Braun Blanquet and de Bolos (1957, Annales Estacion Experimental de Aula Dei, 5, 266). This method has been used to study the floristic diversity represented by the floristic richness, Shannon index, the equitability, the biological and the phytochoric type. The climatic correction according to the altitudinal gradient was applied to determine the bioclimatic stage. The results from the surveys indicate that the rangelands at the studied sites contain 109 species, 27 families and 63 genera out of which 79 species and 22 families are in the semi‐arid bioclimatic stage. A two‐way analysis of variance was employed to examine the effect of the bioclimatic stage and the pasture land put at rest. Variance analysis of the diversity indices showed that the bioclimatic stage has a significant impact on the floristic richness and flora diversity of the S. tenacissima steppe (p ≤ 0.01) with a 5% threshold; on the other hand, the protection of these ecosystems does not have a remarkable influence on the floristic diversity (p > 0.05). In recent years, climatic disturbances have resulted in changes in vegetation, even in rested areas located between the study localities.     

Aphid–willow interactions in a high Arctic ecosystem: responses to raised temperature and goose disturbance

Recently, there have been several studies using open top chambers (OTCs) or cloches to examine the response of Arctic plant communities to artificially elevated temperatures. Few, however, have investigated multitrophic systems, or the effects of both temperature and vertebrate grazing treatments on invertebrates. This study investigated trophic interactions between an herbivorous insect (Sitobion calvulum, Aphididae), a woody perennial host plant (Salix polaris) and a selective vertebrate grazer (barnacle geese, Branta leucopsis). In a factorial experiment, the responses of the insect and its host to elevated temperatures using open top chambers (OTCs) and to three levels of goose grazing pressure were assessed over two summer growing seasons (2004 and 2005). OTCs significantly enhanced the leaf phenology of Salix in both years and there was a significant OTC by goose presence interaction in 2004. Salix leaf number was unaffected by treatments in both years, but OTCs increased leaf size and mass in 2005. Salix reproduction and the phenology of flowers were unaffected by both treatments. Aphid densities were increased by OTCs but unaffected by goose presence in both years. While goose presence had little effect on aphid density or host plant phenology in this system, the OTC effects provide interesting insights into the possibility of phenological synchrony disruption. The advanced phenology of Salix effectively lengthens the growing season for the plant, but despite a close association with leaf maturity, the population dynamics of the aphid appeared to lack a similar phenological response, except for the increased population observed.