Animals are expected to select a breeding habitat using cues that should reflect, directly or not, the fitness outcome of the different habitat options. However, human-induced environmental changes can alter the relationship between habitat characteristics and their fitness consequences, leading to a maladaptive habitat choice. The most severe case of such nonideal habitat selection is the ecological trap, which occurs when individuals prefer to settle in poor-quality habitats while better ones are available. Here we studied the adaptiveness of nest box selection in a tree swallow (Tachycineta bicolor) population breeding over a 10-year period in a network of 400 nest boxes distributed along a gradient of agricultural intensification in southern Québec, Canada. We first examined the effects of multiple environmental and social habitat characteristics on nest box preference to identify potential settlement cues. We then assessed the links between those cues and habitat quality as defined by the reproductive performance of individuals that settled early or late in nest boxes. We found that tree swallows preferred nesting in open habitats with high cover of perennial forage crops, high spring insect biomass, and high density of house sparrows, their main competitors for nest sites. They also preferred nesting where the density of breeders and their mean number of fledglings during the previous year were high. Additionally, we detected mismatches between preference and habitat quality for several environmental variables. The density of competitors and conspecific social information showed severe mismatches, as their relationships to preference and breeding success went in opposite direction under certain circumstances. Spring food availability and agricultural landscape context, while related to preferences, were not related to breeding success. Overall, our study emphasizes the complexity of habitat selection behavior and provides evidence that multiple mechanisms may potentially lead to an ecological trap in farmlands.
The evolution of floral traits is largely attributed to pollinator-mediated selection; however, the importance of pollinators as selective agents in pollen-limited environments is poorly resolved. In pollen-limited arctic and subarctic regions, selection is expected to either favor floral traits that increase pollinator attraction or promote reproductive assurance through selfing. We quantified phenotypic selection on floral traits in two arctic and two subarctic populations of Parrya nudicaulis. Additionally, we measured selection in plants in both open-pollination and pollen-augmentation treatments to estimate selection imposed by pollinators in one population. Seed production was found to be limited by pollen availability and strong directional selection on flower number was observed. We did not detect consistently greater magnitudes of selection on floral traits in the arctic relative to the subarctic populations. Directional selection for more pigmented flowers in one arctic population was observed however. In some populations, selection on flower color was found to interact with other traits. We did not detect consistently stronger selection gradients across all traits for plants exposed to pollinator selection relative to those in the pollen-augmentation treatment; however directional selection tended to be higher for some floral traits in open-pollinated plants.
The timing of germination is a key life-history trait in plants, which is strongly affected by the strength of seed dormancy. Continental-wide variation in seed dormancy has been related to differences in climate and the timing of conditions suitable for seedling establishment. However, for predictions of adaptive potential and consequences of climatic change, information is needed regarding the extent to which seed dormancy varies within climatic regions and the factors driving such variation We planted 17 Italian and 28 Fennoscandian populations of Arabidopsis thaliana in the greenhouse and at two field sites in Italy and Sweden. To identify possible drivers of among-population variation in seed dormancy, we examined the relationship between seed dormancy and climate at the sites where populations were originally sampled. Seed dormancy was on average stronger in the Italian compared to the Fennoscandian populations, but also varied widely within both regions. Estimates of seed dormancy in the three maternal environments were positively correlated, but seeds had on average stronger dormancy when produced in the greenhouse than at the two field sites. Among Fennoscandian populations, seed dormancy tended to increase with increasing summer temperature and decreasing precipitation at the site of origin. In the smaller sample of Italian populations, no significant association was detected between mean seed dormancy and climate at the site of origin. The correlation between seed dormancy and climatic factors in Fennoscandia suggests that at least some of the among-population variation is adaptive and that climate change will affect selection on this trait.
Conservation of large carnivores like leopards requires large and interconnected habitats. Despite the wide geographic range of the leopard globally, only 17% of their habitat is within protected areas. In Nepal, leopards are distributed widely across the country but their status is not adequately studied which compromised the necessary conservation attention for the species. This study carried out sign-based occupancy survey across the Chure (the Himalayan foothills) range (~19,000 km2) to understand the habitat occupancy of leopards along with the covariates affecting their presence. The model-averaged leopard occupancy in the Chure range was 0.5732 (0.0082 SD) with a detection probability of 0.2554 (0.1142 SE). The top model included wild boar, ruggedness, presence of livestock and human population density as covariates. The β coefficient estimate from the model indicated the wild boar was the primary covariate contributing positively to the leopard occupancy followed by the presence of livestock, ruggedness and human population density. The detection probability of leopard was higher outside the protected areas, less in the densely vegetated areas, and higher in the area where there is a presence of livestock. Enhanced law enforcement and mass awareness activities are necessary to reduce poaching/killing of wild ungulates and leopard in the Chure range and to increase leopard occupancy. In addition, maintaining a sufficient natural prey base can contribute to minimize the livestock depredation and hence, decrease the human-leopard conflict in the Chure range.
Adult sex ratio and fecundity are key population parameters in sustainable wildlife management, but inferring these requires estimates of the density of at least three age/sex classes of the population (male and female adults and juveniles). We used an array of 36 wildlife camera traps during 2–3 weeks in autumn prior to harvest during two consecutive years, and recorded white-tailed deer adult males, adult females and fawns from the pictures. Simultaneously, we collected fecal DNA (fDNA) from 92 20mx20m plots placed in 23 clusters of four plots between the camera traps. We identified individuals from fDNA samples with microsatellite markers and estimated the total sex ratio and population density using Spatial Capture Recapture (SCR). The fDNA-SCR analysis concluded equal sex ratio in the first year and female bias in the second year, and no difference in space use between sexes (fawns and adults combined). Camera information was analyzed in a Spatial Capture (SC) framework assuming an informative prior for animals’ space use, either (1) as estimated by fDNA-SCR (same for all age/sex classes), (2) as assumed from the literature (space use of adult males larger than adult females and fawns), (3) by inferring adult male space use from individually-identified males from the camera pictures. These various SC approaches produced plausible inferences on fecundity, but also inferred total density to be lower than the estimate provided by fDNA-SCR in one of the study years. SC approaches where adult male and female were allowed to differ in their space use suggested the population had a female-biased adult sex ratio. In conclusion, SC approaches allowed estimating the pre-harvest population parameters of interest and provided conservative density estimates.
The usage of preprint servers in ecology and evolution is increasing, as it allows for research to be rapidly disseminated and available through open access at no cost. This is relevant for Early Career Researchers (ECRs), who must demonstrate research ability for funding opportunities, scholarships, grants, or faculty positions in short temporal windows in order to advance their careers. Concurrently, limited experience with the peer review process can make it challenging for those who are in the early stages of their research career to build publication records. Therefore, ECRs face different challenges relative to researchers with permanent positions and established research programs and have different requirements in terms of research output and timelines. These challenges might also vary according to institution size and country, which are associated with the availability of funding for open access journals. Herein, we hypothesize that career stage and institution size impact relative usage of preprint servers among researchers in ecology and evolution. Using data collected from 500 articles (100 from each of two open access journals, two closed access journals, and a preprint server), we demonstrate that ECRs generate more preprints relative to non-ECRs, for both first and last authors. We speculate that this pattern is reflective of the advantages of quick and open access research that is disproportionately beneficial to ECRs. There is also a marginal effect of first author institution size on preprint usage, whereby the number of preprints tends to increase with institution size for ECRs, although the interaction between ECR status and institution size was not significant. The United States and United Kingdom contributed the greatest number of preprints by early career researchers, whereas non-western countries contributed relatively fewer preprints. This research provides empirical evidence regarding motivations of preprint usage and barriers surrounding large-scale adoption of preprinting in ecology and evolution.
Collisions with vehicles are a major threat to wildlife populations and often occur in identifiable patterns. To reduce wildlife road mortalities, mitigation structures including exclusionary fencing and wildlife crossings are constructed. Openings in fencing at road intersections may lead to concentration of road mortality hot spots at openings leading to a belief that these gaps concentrate road mortalities. However, it is also possible that hot spots existed at these locations before construction indicating that road mortality patterns have not changed with mitigation structure construction. Therefore, to assess mitigation structure effectiveness, it is important to examine both road mortality numbers and road mortality spatial distribution. Wildlife road mortality data was collected on a 15-km section of rural highway in Texas, USA before, during, and after the construction of wildlife mitigation structures. We expected that the number of road mortalities would decrease after construction compared to before construction and that road mortalities would become more concentrated around openings in the fence. We used ANOVA to compare numbers of road mortalities and emerging hot spot analysis and generalized linear modelling to assess changes in road mortality spatial distribution. Road mortalities were not significantly different in the before and after construction periods (p = 0.092). While there were no significant changes in road mortality patterns with construction, cluster intensity was greater when nearer to fence openings in all three time periods. Emerging hot spot analysis provides an effective and easy way to visualize road mortality patterns through time, however, due to low numbers of mortalities in many road mortality studies, including this one, the power of this analysis to detect significant changes in road mortality may be limited. This technique can provide both ecologists and transportation planners an effective tool for identifying patterns that may warrant further investigation using traditional statistical techniques.
Understanding the role of ecological processes in speciation has become one of the most active areas of research in marine population biology in recent decades. The traditional view was that allopatry was the primary driver of speciation in marine taxa, but the geography of the marine environment and the dispersal capabilities of many marine organisms render this view somewhat questionable. One of the earliest and most highly cited empirical examples of ecological speciation with gene flow in marine fishes is that of the slippery dick wrasse, Halichoeres bivittatus. Evidence for this cryptic or incipient speciation event was primarily in the form of a deep north-south divergence in a single mitochondrial locus, combined with a finding that these two haplotypes were associated with different habitat types in the Florida Keys and Bermuda, where they overlap. Here we examine habitat assortment in the Florida Keys using a broader sampling of populations and habitat types than were available for the original study, and find no evidence to support the claim that haplotype frequencies differ between habitat types, and little evidence to support any differences between populations. These results severely undermine claims of ecological speciation with gene flow in Halichoeres bivittatus. We argue that future claims of this type should be supported by multiple lines of evidence that illuminate potential mechanisms and allow researchers to rule out alternative explanations for spatial patterns of genetic differences.
1. Restoration ecology has historically focused on reconstructing communities of highly visible taxa whilst less visible taxa, such as invertebrates and microbes, are ignored. This is problematic as invertebrates and microbes make up the vast bulk of biodiversity and drive many key ecosystem processes, yet they are rarely actively reintroduced following restoration, potentially limiting ecosystem function and biodiversity in these areas. 2. In this review, we discuss the current (limited) incorporation of invertebrates and microbes in restoration and rewilding projects. We argue that these groups should be actively rewilded during restoration to improve biodiversity and ecosystem function outcomes and highlight how they can be used to greater effect in the future. For example, invertebrates and microbes are easily manipulated, meaning whole communities can potentially be rewilded through habitat transplants in a practice that we refer to as “whole-of-community” rewilding. 3. We provide a framework for whole-of-community rewilding and describe empirical case studies as practical applications of this under-researched restoration tool that land managers can use to improve restoration outcomes. 4. We hope this new perspective on whole-of-community restoration will promote applied research into restoration that incorporates all biota, irrespective of size, whilst also enabling a better understanding of fundamental ecological theory, such as colonisation- competition trade-offs. This may be a necessary consideration as invertebrates that are important in providing ecosystem services are declining globally; targeting invertebrate communities during restoration may be crucial in stemming this decline.
Species delimitation among closely related species is challenging because traditional phenotype-based approaches, e.g., morphology, ecological, or chemical characteristics, often produce conflicting results. With the advent of high-throughput sequencing, it has become increasingly cost-effective to acquire genome-scale data which can resolve previously ambiguous species boundaries. As the availability of genome-scale data has increased, numerous species delimitation analyses, such as BPP and SNAPP+Bayes factor delimitation (BFD*), have been developed to delimit species boundaries. However, even empirical molecular species delimitation approaches can be biased by confounding evolutionary factors, e.g., hybridization/introgression and incomplete lineage sorting, and computational limitations. Here we investigate species boundaries and the potential for micro-endemism in a lineage of lichen-forming fungi, Niebla Rundel & Bowler in the family Ramalinaceae. The species delimitation models tend to support more specious groupings, but were unable to infer robust, consistent species delimitations. The results of our study highlight the problem of delimiting species, particularly in groups such as Niebla, with complex, recent phylogeographic histories.
Resource availability and heterogeneity are recognized as two essential environmental aspects to determine species diversity and community abundance. However, how resource availability and heterogeneity determine species diversity and community abundance in highly heterogeneous and most fragile karst landscapes is largely unknown. We examined the effects of resource availability and heterogeneity on plant community composition and quantified their relative contribution by variation partitioning. Then, a structural equation model (SEM) was used to further disentangle the multiple direct and indirect effects of resource availability on plant community composition. Species diversity was significantly influenced by the resource availability in shrubland and woodland but not by the heterogeneity in woodland. Abundance was significantly affected by both resource availability and heterogeneity, whereas variation partitioning results showed that resource availability explained the majority of the variance in abundance, and the contribution of resource heterogeneity was marginal. These results indicated that resource availability plays a more important role in determining karst plant community composition than resource heterogeneity. Our SEMs further found that the multiple direct and indirect processes of resource availability in determining karst species diversity and abundance were different in different vegetation types. Resource availability and heterogeneity both played a certain role in determining karst plant community composition, while the importance of resource availability far exceeded resource heterogeneity. We propose that steering community restoration and reconstruction should be highly dependent on resource availability, and multiple direct and indirect pathways of resource availability for structuring karst plant communities need to be taken into account.
Guava (Psidium guajava) is one of the most aggressive invasive plants in the Galapagos Islands. Determining its provenance and genetic diversity could provide valuable information for its control. With this purpose, we analyzed 11 SSR markers in guava individuals collected from Isabela, Santa Cruz, San Cristobal and Floreana islands in the Galapagos, as well as from mainland Ecuador. The mainland guava population appeared genetically differentiated from the Galapagos populations, with higher genetic diversity levels found in the former. By using different approaches for data analysis, we consistently found that the Central Highlands region of mainland Ecuador is one of the most likely origins of the Galapagos populations. Moreover, the guavas from Isabela and Floreana show a potential genetic input from southern mainland Ecuador, while the population from San Cristobal would be linked to the coastal mainland regions. Interestingly, the proposed origins for the Galapagos guava coincide with the first human settlings of the archipelago. By employing Approximate Bayesian Computation, we propose a model where San Cristobal was the first island to be colonized by guava from the mainland, from which it would have spread to Floreana and finally to Santa Cruz; Isabela would have been seeded from Floreana. An independent trajectory could also have contributed in the invasion of Floreana and Isabela. The pathway shown in our model agrees with the human colonization history of the different islands in the Galapagos. Our model, in conjunction with the clustering patterns of the guava individuals (based on genetic distances), suggests that guava introduction history in the Galapagos archipelago was driven predominantly by a single event (or events in rapid succession) instead of several independent introductions. We thus show that genetic analyses supported by historical sources can be used to answer questions on the variability and history of guava in the Galapagos Islands.
Adaptations to anthropogenic domestic habitats contribute to the success of mosquito Aedes aegypti as a major global vector of several arboviral diseases. The species inhabited African forests before expanding into domestic habitats and spreading to the rest of the world. Despite a well-studied evolutionary history, how this species initially moved into human settlements in Africa remains unclear. During this initial habitat transition, Ae. aegypti switched from using natural containers like tree holes as larval breeding sites to using artificial containers like clay pots. Little is known about how these natural versus artificial containers differ in their environments, or whether Ae. aegypti in forest versus domestic habitats evolved any corresponding incipient behavioral divergence, such as in oviposition. To address these gaps, we first characterized physical characteristics, larval density, microbial density, bacterial composition, and volatile profiles of natural versus artificial containers used as mosquito larval breeding sites. We focused on two localities in Africa, La Lopé, Gabon and Rabai, Kenya. In both localities, our data showed that the two habitat-specific container types had significantly different characteristics. We then examined whether such containers differed in their attractiveness for oviposition, a key behavior affecting larval distribution. Forest Ae. aegypti readily accepted artificial containers in our field experiments, and laboratory choice experiments did not find distinct oviposition preference between forest and village Ae. aegypti colonies. These results suggested that African Ae. aegypti were likely generalists in their oviposition site choice. This flexibility to accept different containers might play a vital role during the initial domestication of Ae. aegypti, allowing the mosquitoes to use human-stored water as fallback breeding sites during dry seasons. Although ovipositional changes were not present initially, after longer domestic habitat breeding, the mosquitoes did evolve divergence oviposition preference, as suggested by previous comparisons of African Ae. aegypti and human-specialized non-African Ae. aegypti.
Both cognitive abilities and dispersal tendencies can vary strongly between individuals. Since cognitive abilities may help dealing with unknown circumstances it is conceivable that dispersers may rely more heavily on learning abilities than residents. However, cognitive abilities are costly and leaving a familiar place might result in losing the advantage of having learned to deal with local conditions. Thus, individuals which invested in learning to cope with local conditions may be more reluctant to leave their natal place. In order to disentangle the complex relationship between dispersal and learning abilities we implemented individual-based simulations. By allowing for developmental plasticity, individuals could either develop a ‘resident´ or ‘dispersal´ cognitive phenotype. In line with our expectations, the correlation between learning abilities and dispersal could take any direction, depending how much time individuals had to recoup their investment in cognition. Both, longevity and the timing of dispersal within lifecycles determine the time individuals have to recoup that investment and thus crucially influence this correlation. We therefore suggest that species´ life-history will strongly impact the expected cognitive abilities of dispersers, relative to their resident conspecifics, and that cognitive abilities might be an integral part of dispersal syndromes.
To contain transmission of COVID-19, lockdown or strict restriction of people’s mobility outside their residence was imposed worldwide. In Nepal, the first phase of nationwide lockdown was observed from March 24 to July 21, 2020. This sudden halt in human activities brought positive and negative impacts on forests and wildlife. We undertook a study was undertaken to know the impact of the CoViD-19 lockdown on wildlife and forests in the protected areas (PAs) of Nepal. The study was carried in July and September 2020, data of illegal activities recorded by the PAs and also those reported by media were obtained and analyzed. Key Informant Interview (KII) was done with the park officers and security personnel by virtual communication that included telephone, messenger app, and ZOOM video meeting to collect detailed information and for verification. The collected data were categorized into four groups: i) wildlife killed, ii) wildlife injured, iii) arrest incidents related to forest crime, and iv) arrest incidents related to wildlife crime. Data from the fiscal year 2019-2020 were analyzed, comparing before lockdown and after. The study found trends of substantial increases in. wildlife death in two PAs, Banke National Park and Bardia National Park out of 20 during the lockdown. Similarly, Chitwan National Park (CNP) and Shivapuri Nagarjun National Park (SNNP) witnessed a rise in wildlife poaching. CNP and SNNP are located close to highly populated cities and also having human settlements in their peripheries. Interestingly, wildlife was easily sighted inside PAs during the lockdown, presumably because the absence of visitors and human activities during the lockdown decreased disturbance. Thus, a paradoxical situation was observed with the wildlife enjoying the freedom of movement on the one hand, but with poachers, many of them laid off from other activities, taking advantage of the lapse in security.
Large-scale patterns of biodiversity and the underlying mechanisms that regulate these patterns are central topics in biogeography and macroecology. The Qinghai-Tibetan Plateau (QTP) is a natural laboratory for studying these issues. However, most previous studies have focused on the entire QTP, and the independent physical geographical subunits in the region are not well understood. We studied the current plant diversity on the Kunlun Mountains, an independent physical geographical subunit located in northwest China, on the northern edge of the QTP. We integrated measures of species distribution, geological history, and phylogeography, and analyzed the taxonomic richness, origin time, and community phylogenetic structure of the plants present in the area. The distribution patterns of 1,911 seed plants highlighted that species were located mainly in the eastern regions of the Kunlun Mountains. Chinese endemic species of seed plants accounted for 29.8% of the total species on the Kunlun Mountains. The biodiversity patterns and mean divergence times (MDT) indicated that the eastern region of the Kunlun Mountains was the center for biodiversity conservation, particularly in the southeastern region, which has served as a museum for plant diversity on the Kunlun Mountains. According to the MDT, the origin time of the Kunlun Mountains’ flora (KMF) was early Miocene (19.40 Ma), and the KMF is ancient. The biogeographical roles of the Kunlun Mountains were corridor and sink, and the corresponding key processes were species immigration and extinction. The extant biodiversity on the Kunlun Mountains has occurred through species recolonization after climatic fluctuations and glaciations during the Quaternary. The Kunlun Mountains also formed a barrier, representing a boundary among multiple floras, and converted the QTP into a closed physical geographical unit. The nearest taxon index indicated that habitat filtering may have played an important role in biodiversity patterns.
1. The COVID-19 pandemic has highlighted the importance of efficient sampling strategies and statistical methods for monitoring infection prevalence, both in humans and reservoir hosts. Pooled testing can be an efficient tool for learning pathogen prevalence in a population. Typically pooled testing requires a second phase follow up procedure to identify infected individuals, but when the goal is solely to learn prevalence in a population, such as a reservoir host, there are more efficient methods for allocating the second phase samples. 2. To estimate pathogen prevalence in a population, this manuscript presents an approach for data integration with two-phased testing of pooled samples that allows more efficient estimation of prevalence with less samples than traditional methods. The first phase uses pooled samples to estimate the population prevalence and inform efficient strategies for the second phase. To combine information from both phases, we introduce a Bayesian data integration procedure that combines pooled samples with individual samples for joint inferences about the population prevalence. 3. Data integration procedures result in more efficient estimation of prevalence than traditional procedures that only use individual samples or a single phase of pooled sampling. 4. The manuscript presents guidance on implementing the first phase and second phase sampling plans using data integration. Such methods can be used to assess the risk of pathogen spillover from reservoir hosts to humans, or to track pathogens such as SARS-CoV-2 in populations.