Generalist trophic ecology in a changing habitat: The case of the four‐striped mouse in a woody‐encroached savannah

Trophic generalists tolerate greater habitat change than specialists; however, few studies explore how generalist trophic ecology is affected. We established how the trophic ecology of an extreme generalist, Rhabdomys pumilio, changed in relation to a directionally changing woody‐encroached savannah in Eastern Cape, South Africa by investigating (a) foraging behaviour, (b) trophic niche and (c) feedback effects. (a) Giving‐up densities showed that R. pumilio preferred foraging in subcanopy microhabitat during the night as a result of lower thermoregulatory costs, but had similar preferences for sub‐ and intercanopy microhabitats during the day. (b) An isotope analysis revealed that the dietary composition and trophic niche occupied by R. pumilio differed among tree canopy cover levels (0%, 30% and 80%), which appeared to be related to changes in C₄ grass material and invertebrate availability. (c) Artificial seed patches suggested that R. pumilio was a potentially important postdispersal seed predator of the woody‐encroaching species, Vachellia karroo. Thus, an increase in tree canopy cover altered the trophic niche of R. pumilio by reducing foraging costs at night and providing alternative food resources in terms of availability and source. These findings demonstrate how an extreme generalist adapted to human‐induced habitat change through changes in its trophic ecology.     

Post‐fragmentation population structure in a cooperative breeding Afrotropical cloud forest bird: emergence of a source‐sink population network

The impact of demographic parameters on the genetic population structure and viability of organisms is a long‐standing issue in the study of fragmented populations. Demographic and genetic tools are now readily available to estimate census and effective population sizes and migration and gene flow rates with increasing precision. Here we analysed the demography and genetic population structure over a recent 15‐year time span in five remnant populations of Cabanis's greenbul (Phyllastrephus cabanisi), a cooperative breeding bird in a severely fragmented cloud forest habitat. Contrary to our expectation, genetic admixture and effective population sizes slightly increased, rather than decreased between our two sampling periods. In spite of small effective population sizes in tiny forest remnants, none of the populations showed evidence of a recent population bottleneck. Approximate Bayesian modelling, however, suggested that differentiation of the populations coincided at least partially with an episode of habitat fragmentation. The ratio of meta‐N_e to meta‐N_c was relatively low for birds, which is expected for cooperative breeding species, while N_e/N_c ratios strongly varied among local populations. While the overall trend of increasing population sizes and genetic admixture may suggest that Cabanis's greenbuls increasingly cope with fragmentation, the time period over which these trends were documented is rather short relative to the average longevity of tropical species. Furthermore, the critically low N_c in the small forest remnants keep the species prone to demographic and environmental stochasticity, and it remains open if, and to what extent, its cooperative breeding behaviour helps to buffer such effects.     

Hybridization selects for prime‐numbered life cycles in Magicicada: An individual‐based simulation model of a structured periodical cicada population

We investigate competition between separate periodical cicada populations each possessing different life‐cycle lengths. We build an individual‐based model to simulate the cicada life cycle and allow random migrations to occur between patches inhabited by the different populations. We show that if hybridization between different cycle lengths produces offspring that have an intermediate life‐cycle length, then predation acts disproportionately to select against the hybrid offspring. This happens because they emerge in low densities without the safety‐in‐numbers provided by either parent population. Thus, prime‐numbered life cycles that can better avoid hybridization are favored. However, we find that this advantage of prime‐numbered cycles occurs only if there is some mechanism that can occasionally synchronize emergence between local populations in sufficiently many patches.     

The devil is in the detail: Nonadditive and context‐dependent plant population responses to increasing temperature and precipitation

In climate change ecology, simplistic research approaches may yield unrealistically simplistic answers to often more complicated problems. In particular, the complexity of vegetation responses to global climate change begs a better understanding of the impacts of concomitant changes in several climatic drivers, how these impacts vary across different climatic contexts, and of the demographic processes underlying population changes. Using a replicated, factorial, whole‐community transplant experiment, we investigated regional variation in demographic responses of plant populations to increased temperature and/or precipitation. Across four perennial forb species and 12 sites, we found strong responses to both temperature and precipitation change. Changes in population growth rates were mainly due to changes in survival and clonality. In three of the four study species, the combined increase in temperature and precipitation reflected nonadditive, antagonistic interactions of the single climatic changes for population growth rate and survival, while the interactions were additive and synergistic for clonality. This disparity affects the persistence of genotypes, but also suggests that the mechanisms behind the responses of the vital rates differ. In addition, survival effects varied systematically with climatic context, with wetter and warmer + wetter transplants showing less positive or more negative responses at warmer sites. The detailed demographic approach yields important mechanistic insights into how concomitant changes in temperature and precipitation affect plants, which makes our results generalizable beyond the four study species. Our comprehensive study design illustrates the power of replicated field experiments in disentangling the complex relationships and patterns that govern climate change impacts across real‐world species and landscapes.     

netview p: a network visualization tool to unravel complex population structure using genome‐wide SNPs

Network‐based approaches are emerging as valuable tools for the analysis of complex genetic structure in wild and captive populations. netview p combines data quality control with the construction of population networks through mutual k‐nearest neighbours thresholds applied to genome‐wide SNPs. The program is cross‐platform compatible, open‐source and efficiently operates on data ranging from hundreds to hundreds of thousands of SNPs. The pipeline was used for the analysis of pedigree data from simulated (n = 750, SNPs = 1279) and captive silver‐lipped pearl oysters (n = 415, SNPs = 1107), wild populations of the European hake from the Atlantic and Mediterranean (n = 834, SNPs = 380) and grey wolves from North America (n = 239, SNPs = 78 255). The population networks effectively visualize large‐ and fine‐scale genetic structure within and between populations, including family‐level structure and relationships. netview p comprises a network‐based addition to other population analysis tools and provides user‐friendly access to a complex network analysis pipeline through implementation in python .     

Variations in age‐ and sex‐specific survival rates help explain population trend in a discrete marine mammal population

Understanding the drivers underlying fluctuations in the size of animal populations is central to ecology, conservation biology, and wildlife management. Reliable estimates of survival probabilities are key to population viability assessments, and patterns of variation in survival can help inferring the causal factors behind detected changes in population size. We investigated whether variation in age‐ and sex‐specific survival probabilities could help explain the increasing trend in population size detected in a small, discrete population of bottlenose dolphins Tursiops truncatus off the east coast of Scotland. To estimate annual survival probabilities, we applied capture–recapture models to photoidentification data collected from 1989 to 2015. We used robust design models accounting for temporary emigration to estimate juvenile and adult survival, multistate models to estimate sex‐specific survival, and age models to estimate calf survival. We found strong support for an increase in juvenile/adult annual survival from 93.1% to 96.0% over the study period, most likely caused by a change in juvenile survival. Examination of sex‐specific variation showed weaker support for this trend being a result of increasing female survival, which was overall higher than for males and animals of unknown sex. Calf survival was lower in the first than second year; a bias in estimating third‐year survival will likely exist in similar studies. There was some support first‐born calf survival being lower than for calves born subsequently. Coastal marine mammal populations are subject to the impacts of environmental change, increasing anthropogenic disturbance and the effects of management measures. Survival estimates are essential to improve our understanding of population dynamics and help predict how future pressures may impact populations, but obtaining robust information on the life history of long‐lived species is challenging. Our study illustrates how knowledge of survival can be increased by applying a robust analytical framework to photoidentification data.     

Population genomics reveals multiple drivers of population differentiation in a sex‐role‐reversed pipefish

A major goal of molecular ecology is to identify the causes of genetic and phenotypic differentiation among populations. Population genomics is suitably poised to tackle these key questions by diagnosing the evolutionary mechanisms driving divergence in nature. Here, we set out to investigate the evolutionary processes underlying population differentiation in the Gulf pipefish, Syngnathus scovelli. We sampled approximately 50 fish from each of 12 populations distributed from the Gulf coast of Texas to the Atlantic coast of Florida and performed restriction‐site‐associated DNA sequencing to identify SNPs throughout the genome. After imposing quality and stringency filters, we selected a panel of 6348 SNPs present in all 12 populations, 1753 of which were not physically linked. We identified a genome‐wide pattern of isolation by distance, in addition to a more substantial genetic break separating populations in the Gulf of Mexico from those in the Atlantic. We also used several divergence outlier approaches and tests for genotype–environment correlations to identify 400 SNPs putatively involved in local adaptation. Patterns of phenotypic differentiation and variation diverged from the overall genomic pattern, suggesting that selection, phenotypic plasticity or demographic factors may be shaping phenotypes in distinct populations. Overall, our results suggest that population divergence is driven by a variety of factors in S. scovelli, including neutral processes and selection on multiple traits.     

Assessing forest vulnerability to climate warming using a process‐based model of tree growth: bad prospects for rear‐edges

Growth models can be used to assess forest vulnerability to climate warming. If global warming amplifies water deficit in drought‐prone areas, tree populations located at the driest and southernmost distribution limits (rear‐edges) should be particularly threatened. Here, we address these statements by analyzing and projecting growth responses to climate of three major tree species (silver fir, Abies alba; Scots pine, Pinus sylvestris; and mountain pine, Pinus uncinata) in mountainous areas of NE Spain. This region is subjected to Mediterranean continental conditions, it encompasses wide climatic, topographic and environmental gradients, and, more importantly, it includes rear‐edges of the continuous distributions of these tree species. We used tree‐ring width data from a network of 110 forests in combination with the process‐based Vaganov–Shashkin‐Lite growth model and climate–growth analyses to forecast changes in tree growth during the 21st century. Climatic projections were based on four ensembles CO₂ emission scenarios. Warm and dry conditions during the growing season constrain silver fir and Scots pine growth, particularly at the species rear‐edge. By contrast, growth of high‐elevation mountain pine forests is enhanced by climate warming. The emission scenario (RCP 8.5) corresponding to the most pronounced warming (+1.4 to 4.8 °C) forecasted mean growth reductions of ?10.7% and ?16.4% in silver fir and Scots pine, respectively, after 2050. This indicates that rising temperatures could amplify drought stress and thus constrain the growth of silver fir and Scots pine rear‐edge populations growing at xeric sites. Contrastingly, mountain pine growth is expected to increase by +12.5% due to a longer and warmer growing season. The projections of growth reduction in silver fir and Scots pine portend dieback and a contraction of their species distribution areas through potential local extinctions of the most vulnerable driest rear‐edge stands. Our modeling approach provides accessible tools to evaluate forest vulnerability to warmer conditions.     

A novel approach to parasite population genetics: Experimental infection reveals geographic differentiation,recombination and host‐mediated population structure in Pasteuria ramosa,a bacterial parasite of Daphnia

The population structure of parasites is central to the ecology and evolution of host‐parasite systems. Here, we investigate the population genetics of Pasteuria ramosa, a bacterial parasite of Daphnia. We used natural P. ramosa spore banks from the sediments of two geographically well‐separated ponds to experimentally infect a panel of Daphnia magna host clones whose resistance phenotypes were previously known. In this way, we were able to assess the population structure of P. ramosa based on geography, host resistance phenotype and host genotype. Overall, genetic diversity of P. ramosa was high, and nearly all infected D. magna hosted more than one parasite haplotype. On the basis of the observation of recombinant haplotypes and relatively low levels of linkage disequilibrium, we conclude that P. ramosa engages in substantial recombination. Isolates were strongly differentiated by pond, indicating that gene flow is spatially restricted. Pasteuria ramosa isolates within one pond were segregated completely based on the resistance phenotype of the host—a result that, to our knowledge, has not been previously reported for a nonhuman parasite. To assess the comparability of experimental infections with natural P. ramosa isolates, we examined the population structure of naturally infected D. magna native to one of the two source ponds. We found that experimental and natural infections of the same host resistance phenotype from the same source pond were indistinguishable, indicating that experimental infections provide a means to representatively sample the diversity of P. ramosa while reducing the sampling bias often associated with studies of parasite epidemics. These results expand our knowledge of this model parasite, provide important context for the large existing body of research on this system and will guide the design of future studies of this host‐parasite system.     

Slow life history and rapid extreme flood: demographic mechanisms and their consequences on population viability in a threatened amphibian

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Simulating evolutionary responses of an introgressed insect resistance trait for ecological effect assessment of transgene flow: a model for supporting informed decision‐making in environmental risk assessment

Predicting outcomes of transgene flow from arable crops requires a system perspective that considers ecological and evolutionary processes within a landscape context. In Europe, the arable weed Raphanus raphanistrum is a potential hybridization partner of oilseed rape, and the two species are ecologically linked through the common herbivores Meligethes spp. Observations in Switzerland show that high densities of Meligethes beetles maintained by oilseed rape crops can lead to considerable damage on R. raphanistrum. We asked how increased insect resistance in R. raphanistrum – as might be acquired through introgression from transgenic oilseed rape – would affect seed production under natural herbivore pressure. In simulation experiments, plants protected against Meligethes beetles produced about twice as many seeds as unprotected plants. All stages in the development of reproductive structures from buds to pods were negatively affected by the herbivore, with the transition from buds to flowers being the most vulnerable. We conclude that resistance to Meligethes beetles could confer a considerable selective advantage upon R. raphanistrum in regions where oilseed rape is widely grown.     

Wrong place,wrong time: climate change‐induced range shift across fragmented habitat causes maladaptation and declined population size in a modelled bird species

Many species are locally adapted to decreased habitat quality at their range margins, and therefore show genetic differences throughout their ranges. Under contemporary climate change, range shifts may affect evolutionary processes at the expanding range margin due to founder events. In addition, populations that are affected by such founder events will, in the course of time, become located in the range centre. Recent studies investigated evolutionary changes at the expanding range margin, but have not assessed eventual effects across the species' range. We explored the possible influence of range shift on the level of adaptation throughout the species' total range. For this we used a spatially explicit, individual‐based simulation model of a woodland bird, parameterized after the middle spotted woodpecker ( Dendrocopos medius) in fragmented habitat. We simulated its range under climate change, and incorporated genetic differences at a single locus that determined the individual's degree of adaptation to optimal temperature conditions. Generalist individuals had a large thermal tolerance, but relatively low overall fitness, whereas climate specialists had high fitness combined with a small thermal tolerance. In equilibrium, the populations in the range centre were comprised of the specialists, whereas the generalists dominated the margins. In contrast, under temperature increase, the generalist numbers increased at the expanding margin and eventually also occupied the centre of the shifting range, whereas the specialists were located in the retracting margins. This was caused by founder events and led to overall maladaptation of the species, which resulted in a reduced metapopulation size and thus impeded the species' persistence. We therefore found no evidence for a complementary effect of local adaptation and range shifts on species' survival. Instead, we showed that founder events can cause local maladaptation which can amplify throughout the species' range, and, as such, hamper the species' persistence under climate change.     

Mark‐recapture modeling accounting for state uncertainty provides concurrent estimates of survival and fecundity in a protected harbor seal population

Harbor seal breeding behavior and habitats constrain opportunities for individual‐based studies, and no current estimates of both survival and fecundity exist for any of the populations studied worldwide. As a result, the drivers underlying the variable trends in abundance exhibited by harbor seal populations around the world remain uncertain. We developed an individual‐based study of harbor seals in northeast Scotland, whereby data were collected during daily photo‐identification surveys throughout the pupping seasons between 2006 and 2011. However, a consequence of observing seals remotely meant that information on sex, maturity‐stage, or breeding status was not always available. To provide unbiased estimates of survival rates we conditioned initial release of individuals on the first time sex was known to estimate sex‐specific survival rates, while a robust design multistate model accounting for uncertainty in breeding status was used to estimate reproductive rate of multiparous and ≥3‐yr‐old females. Survival rates were estimated at 0.95 (95% CI = 0.91–0.97) for females and 0.92 (0.83–0.96) for males, while reproductive rate was estimated at 0.89 (0.75–0.95) for multiparous and 0.69 (0.64–0.74) for ≥3‐yr‐old females. Stage‐based population modeling indicated that this population should be recovering, even under the current shooting quotas implemented by the recent management plan.     

Variation in thermal niche of a declining river‐breeding frog: From counter‐gradient responses to population distribution patterns

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Shifts in population size structure for a drying‐tolerant fish in response to extreme drought

For freshwater systems, climate change‐induced alterations to drought regimes are a considerable threat to already threatened species. This is particularly poignant for kōwaro (or Canterbury mudfish, Neochanna burrowsius), a critically endangered fish largely restricted to drying‐prone waterways on the Canterbury Plains, New Zealand. By comparing three catchment‐wide surveys (2007, 2010, 2015) within the Waianiwaniwa Valley, we assessed the scale and magnitude of population change induced by 2 years of consecutive drought (2014–15), when compared to surveys during wetter conditions (2007, 2010). The droughts triggered a catchment‐wide switch from adult‐dominated populations to populations comprised of juveniles indicated by a significant reduction in median size (~95 mm during the wet to ~60 mm after drought). In comparison, population abundances were highly variable, indicated by no significant change in catch‐per‐unit‐effort. The large variation in catch rates and connection of median size to reproductive potential mean median size will be useful to measure in monitoring to infer potential changes to population resilience, particularly during extreme events. Furthermore, because N. burrowsius could be regarded as extremophile fish, already restricted to harsh habitats, they are likely to become increasingly threatened by climate change. Thus, tools that allow for insightful comparisons between populations, such as a population resilience framework based on both abundance and body size distribution, will be increasingly important for pragmatic decision‐making for targeted conservation measures.     

Silicon amendment to rice plants contributes to reduced feeding in a phloem‐sucking insect through modulation of callose deposition

Silicon (Si) uptake by Poaceae plants has beneficial effects on herbivore defense. Increased plant physical barrier and altered herbivorous feeding behaviors are documented to reduce herbivorous arthropod feeding and contribute to enhanced plant defense. Here, we show that Si amendment to rice (Oryza sativa) plants contributes to reduced feeding in a phloem feeder, the brown planthopper (Nilaparvata lugens, BPH), through modulation of callose deposition. We associated the temporal dynamics of BPH feeding with callose deposition on sieve plates and further with callose synthase and hydrolase gene expression in plants amended with Si. Biological assays revealed that BPH feeding was lower in Si‐amended than in nonamended plants in the early stages post‐BPH infestation. Histological observation showed that BPH infestation triggered fast and strong callose deposition in Si‐amended plants compared with nonamended plants. Analysis using qRT‐PCR revealed that expression of the callose synthase gene OsGSL1 was up‐regulated more and that the callose hydrolase (β‐1,3‐glucanase) gene Gns5 was up‐regulated less in Si‐amended than in nonamended plants during the initial stages of BPH infestation. These dynamic expression levels of OsGSL1 and Gns5 in response to BPH infestation correspond to callose deposition patterns in Si‐amended versus nonamended plants. It is demonstrated here that BPH infestation triggers differential gene expression associated with callose synthesis and hydrolysis in Si‐amended and nonamended rice plants, which allows callose to be deposited more on sieve tubes and sieve tube occlusions to be maintained more thus contributing to reduced BPH feeding on Si‐amended plants.     

Contrasting responses to Pleistocene climate changes: a case study of two sister species Allium cyathophorum and A. spicata (Amaryllidaceae) distributed in the eastern and western Qinghai–Tibet Plateau

It has been hypothesized that species occurring in the eastern and the western Qinghai–Tibet Plateau (QTP) responded differently to climate changes during the Pleistocene. Here, we test this hypothesis by phylogeographic analysis of two sister species, Allium cyathophorum and A. spicata. We sequenced two chloroplast DNA (cpDNA) fragments (accD‐psaI and the rpl16 intron) of 150 individuals, and the nuclear (ITS) region of 114 individuals, from 19 populations throughout the distributional ranges of these species. The divergence between the two species was dated at 779 ‐ 714 thousand years before the present and was likely initiated by the most major glaciation in the QTP. Analysis of chlorotype diversity showed that A. spicata, the species occurring in the western QTP, contains much lower genetic diversity (0.25) than A. cyathophorum (0.93), which is distributed in the eastern QTP. Moreover, multiple independent tests suggested that the A. spicata population had expanded recently, while no such expansion was detected in A. cyathophorum, indicating a contrasting pattern of responses to Pleistocene climate changes. These findings highlight the importance of geographical topography in determining how species responded to the climate changes that took place in the QTP during the Pleistocene.