The intestinal microbiota play an important role in the life of amphibians. The composition of the intestinal microbial community may vary by developmental stage. In this study, 16S rRNA high-throughput sequencing was used to study the intestinal microbiota of Hynobius maoershanensis tadpoles and adults that exclusively inhabit the Maoer Mountain swamp at an altitude of approximately 2000 m. The results indicated that there was no significant difference in intestinal microbiota between tadpoles and adults. Nevertheless, the abundance of intestinal microbiota in adults was much higher than that in tadpoles. Specifically, at the phylum level, Bacteroidetes was more abundant in adults than in tadpoles. At the genus level, Proteobacteria, Actinobacteria, Cyanobacteria, and Planctomycetes were more abundant in tadpoles, whereas Burkholderiaceae, Caedibacter, Bacteroides, and Serratia were more abundant in adults. A functional prediction analysis revealed that there was no significant difference between tadpoles and adults; however, the function of the intestinal microbiota in H. maoershanensis includes amino acid transport and metabolism, general function prediction only, transcription, energy production and conversion, liquid transport, and metabolism. The aquatic and terrestrial living environment of tadpoles and adults may be the main reason for the difference in intestinal microbiota between tadpoles and adults. Our study provides evidence of variations in the intestinal microbiota of tadpoles and adult amphibians, highlighting the influence of historical developments on the intestinal microbiota and the need for increased understanding of the importance of physiological characteristics in shaping intestinal microbiota of amphibians, which consequently help us to understand the adaptative mechanism of amphibians from an aquatic to a terrestrial environment.
Prey evolve anti-predator strategies against multiple enemies in nature. We examined how a prey species adopts different predation avoidance tactics against pursuit or sit-and-wait predators. As prey, we used two strains of Tribolium beetles artificially selected for short or long duration of death feigning. The results showed that, as prey, the short strains displayed the same behavior, escaping, against the two types of predators. On the other hand, death feigning is known to be effective for evading a jumping spider in the case of the long strains, while the present study showed that the long strain beetles used freezing behavior against a sit-and-wait type predator A. venator in this study. The short strain beetles were more easily orientated by predators and suffered a higher rate of predation than the long strains. The time to predation was also shorter in the short strains compared to the long strains. When the predator was starved, even the long strains were preyed upon when the predator was orientated toward the prey, suggesting the starvation period, i.e., prey density, is an important factor for antipredator behavior. Traditionally, death feigning has been thought to be the last resort in a series of anti-predator avoidance behaviors. However, our results showed that freezing and death feigning were not parts of a series of behavior, but independent behaviors against different predators, at least for these beetles. The results also suggest that the differences in feeding rates between the strains could be explained by differences in activity among the strains.
To provide the most comprehensive picture of species phylogeny and phylogeography of European roe deer (Capreolus capreolus), we analysed mtDNA control region (610 bp) of 1469 samples of roe deer from Central and Eastern Europe and included into the analyses additional 1541 mtDNA sequences from GenBank from other regions of the continent. We detected two mtDNA lineages of the species: European and Siberian one (an introgression of C. pygargus mtDNA into C. capreolus). The Siberian lineage was most frequent in eastern part of the continent and declined towards Central Europe. The European lineage contained three clades (Central, Eastern and Western) composed of 2 to 8 subclades, many of which were separated in space. The Western clade appeared to have a discontinuous range from Portugal to Russia. Most of the subclades in the Central and the Eastern clades were under expansion during the Weichselian glacial period before the Last Glacial Maximum (LGM), while the expansion time of the Western clade overlapped with the Eemian interglacial. High genetic diversity of extant roe deer is the result of their survival during the LGM in a large, contiguous range spanning from the Iberian Peninsula to the Caucasus Mts. and in two northern refugia.
Acute exposure to warming temperatures increases minimum energetic requirements in ectotherms. However, over and within multiple generations, increased temperatures may cause plastic and evolved changes that modify the temperature sensitivity of energy demand and alter individual behaviours. Here, we aimed to test whether populations recently exposed to geothermally elevated temperatures express an altered temperature sensitivity of metabolism and behaviour. We expected that long-term exposure to warming would moderate metabolic rate, reducing the temperature sensitivity of metabolism, with concomitant reductions in boldness and activity. We compared the temperature sensitivity of metabolic rate (acclimation at 20 versus 30°C) and allometric slopes of routine, standard, and maximum metabolic rates, in addition to boldness and activity behaviours, across eight recently divergent populations of a widespread fish species (Gambusia affinis). Our data reveal that warm-source populations express a reduced temperature sensitivity of metabolism, with relatively high metabolic rates at cool acclimation temperatures and relatively low metabolic rates at warm acclimation temperatures. Allometric scaling of metabolism did not differ with thermal history. Across individuals from all populations combined, higher metabolic rates were associated with higher boldness and activity. However, warm-source populations displayed relatively more bold behaviour at both acclimation temperatures, despite their relatively low metabolic rates at warm acclimation temperatures. Overall, our data suggest that in response to warming, multigenerational processes may not direct trait change along a simple “pace-of-life syndrome” axis, instead causing relative decreases in metabolism and increases in boldness. Ultimately, our data suggest that multigenerational warming may produce a novel combination of physiological and behavioural traits, with consequences for animal performance in a warming world.
Oxford Nanopore Technologies (ONT) is a third-generation sequencing technology that is gaining popularity in ecological research for its portable and low-cost sequencing possibilities. Although the technology is primarily developed for long-read sequencing, it can also be applied to sequence amplicons. The downside of ONT is the low quality of the raw reads. Hence, generating a high-quality consensus sequence is still a challenge. We present Amplicon_sorter, a tool for reference-free sorting of ONT sequenced amplicons based on their similarity in sequence and length and for building solid consensus sequences.
Runs of homozygosity (ROH) are continuous homozygous segments that arise through the transmission of haplotypes that are identical by descent (IBD). The length and distribution of ROH segments provide insight into the genetic diversity of populations and are useful to detect selection signatures. Here, we analysed pooled whole-genome sequencing data from 265 Western honey bee colonies from the two subspecies Apis mellifera mellifera and Apis mellifera carnica. Integrating individual ROH patterns and admixture levels in a high-resolution population network visualization allowed us to ascertain major differences between the two subspecies. Within A. m. mellifera, we identified well-defined substructures according to the genetic origin of the colonies and a fair amount of admixed colonies, despite the current applied conservation efforts. In contrast, A. m. carnica colonies were more inbred and could not be differentiated according to the geographical origin. We identified 29 coding genes in overlapping ROH segments within the two subspecies. Genes embedded in A. m. carnica specific homozygosity islands suggested a strong selection for production and behavioural traits, whilst the identified cuticula protein-coding genes (CPR3 and CPR4) were associated with their breed-specific stripe pattern. Local adaption of the two subspecies could be confirmed by the identification of two genes involved in the response to ultraviolet (UV) light. We demonstrated that colony genotypes derived from pooled honey bee workers are reliable to unravel the population dynamics in A. mellifera and provide fundamental information to conserve native honey bees.
High elevation grasslands provide critical services in agriculture and ecosystem stabilization. However, these ecosystems face elevated risks of disturbance due to predicted soil and climate changes. We experimentally exposed model grassland communities, comprised of three species grown on either local or reference soil, to varied climatic environments along an elevational gradient in the European Alps, measuring the effects on species and community traits. Although species-specific biomass varied across soil and climate, species’ proportional contributions to community-level biomass production remained consistent. Where species experienced low survivorship, species-specific biomass production was maintained through increased production of surviving individuals. Species responded directionally to climatic variation, segregating differentially by plant traits (including height, reproduction, biomass, survival, leaf dry weight, and leaf area) across all sites. Local soil variation drove stochastic trait responses across all species. This soil variability obscured climate-driven responses: we recorded no directional trait responses driven by climate. Our species-based approach contributes to our understanding of grassland community stabilization and suggests that these communities show some stability under climatic variation.
1. Context and need for work The effects and extent of the impacts of agricultural insect pests in and around cropping systems is a rich field of study. However, little research exists on the presence and consequence of pest insects in undisturbed landscapes distant from crop hosts. Research in such areas may yield novel or key insights on pest behavior or ecology that is not evident from agroecosystem-based studies. 2. Approach and methods Using the invasive fruit pest Drosophila suzukii (Matsumura) as a case study, we investigated the presence and resource use patterns of this agricultural pest in wild blackberries growing within the southern Appalachian Mountain range of North Carolina over two years. 3. Main results We found D. suzukii throughout the sampled range with higher levels of infestation (D. suzukii eggs/g fruit) in all ripeness stages in natural areas as compared to cultivated blackberry samples, but especially in under-ripe fruit. 4. Main results We also explored a direct comparison of oviposition preference between wild and cultivated fruit and found higher oviposition in wild berries when equal weights of fruit were offered, but oviposition was higher in cultivated berries when fruit number was equal. 5. Synthesis and applications D. suzukii were wide-spread in previously unsampled remote, forest habitats. Forest populations laid more eggs in unripe wild-grown blackberries throughout the year than populations infesting cultivated berries. This suggests D. suzukii may change its oviposition and foraging behavior in relation to fruit type. Additionally, as D. suzukii exploits a common forest fruit prior to ripeness, further research is needed to explore how this affects wild food web dynamics and spillover to regional agroecosystems.
Once widespread throughout the tropical forests of the Indian Subcontinent, the sloth bears have suffered a rapid range collapse and local extirpations in the recent decades. A significant portion of their current distribution range is situated outside of the protected areas (PAs). These unprotected sloth bear populations are under tremendous human pressures, but little is known about the patterns and determinants of their occurrence in most of these regions. The situation is more prevalent in Nepal where virtually no systematic information is available for sloth bears living outside of the PAs. We undertook a sign survey-based single-season occupancy study intending to overcome this information gap for the sloth bear populations residing in the Trijuga forest of southeast Nepal. Sloth bear sign detection/non-detection data and field-based covariates data were collected at the 74 randomly chosen 4-km2 grid cells using a varying number of 400m long transects in each grid cell. From our results, the model-averaged estimate of site use probability (ψ ± SE) was estimated to be 0.432 ± 0.039, which is a 13% increase from the naïve estimate (0.297) not accounting for imperfect detections of sloth bear signs. The presence of termite mounds and the distance to the nearest water source were the most important variables affecting the habitat use probability of sloth bears. The average site-level detectability (p ± SE) of sloth bear signs was estimated to be 0.195 ± 0.003 and was significantly determined by the index of human disturbances. We recommend considering the importance of fine-scale ecological and anthropogenic factors in predicting the sloth bear-habitat relationships across their range in the Churia habitat of Nepal.
Insect pollinators are important means for a stable ecosystem. The habitat types play a crucial role in the community composition, abundance, diversity, and species richness of the pollinators. The present study in Shivapuri–Nagarjun National Park explored the species richness and abundances of insect pollinators in four different habitats and different environmental variables in determining the community composition of the pollinators. Data were collected from 1500 m–2700 m using pan traps and hand sweeping methods. Non–metric multidimensional scaling (NMDS) and redundancy analysis (RDA) were conducted to show the association between insect pollinators and environmental variables. The results firmly demonstrated that species richness and abundances were higher in open trails compared to other habitats. The distribution of the pollinator species was more uniform in the open trail followed by the grassland. Similarly, a strong positive correlation between flower resources and pollinator’s abundance was found. In conclusion, the open trail harbor rich insect pollinators in lower elevation. The community structure of the pollinators was strongly influenced by the presence of flowers in the trails.
The timing of different life history events are often correlated, and selection might only rarely be exerted independently on the timing of a single event. In plants, phenotypic selection has often been shown to favour earlier flowering. However, little is known about to what extent this selection acts directly vs. indirectly via vegetative phenology, and if selection on the two traits is correlational. We estimated direct, indirect and correlational phenotypic selection on vegetative and reproductive phenology over three years for the perennial herb Lathyrus vernus. Direct selection favoured earlier flowering and shorter timespans between leaf-out and flowering in all years. However, early flowering was associated with early leaf-out, and the direction of selection on leaf-out day varied among years. As a result, selection on leaf-out weakened selection for early flowering in one of the study years. We found no evidence of correlational selection. Our results highlight the importance of including temporally correlated traits when exploring selection on the phenology of seasonal events.
The natural regeneration of native broadleaved species underneath forest monoculture plantations is important to recover ecosystem functions and to mitigate adverse environmental effects. To understand how seed rain and soil seed banks facilitate natural regeneration, we surveyed their density and composition in a monoculture Chinese fir plantation, a mixed Chinese fir–broadleaf plantation, and an adjacent natural broadleaved forest for two years in southern China. Twenty-eight species (16 families) were in seed rain, and 45 species (27 families) were in soil seed banks. Seed rain density did not differ significantly across stands; however, the number of taxa in seed rain was highest in the mixed plantation and lowest in the natural forest. Seed bank density was significantly higher in the mixed plantation than in the other stands. The Sørensen similarity indices of species composition between seed sources and aboveground vegetation were relatively low (<0.50). In addition, the seeds of native tree species common to the seed banks of the three forests indicated the adjacent natural forest was a seed source for the natural regeneration of native species in forest plantations. To augment regeneration and accelerate the rate of conversion, we recommend direct seeding or planting of desired species.
1. Kānuka (Kunzea serotina, Myrtaceae) dryland shrubland communities of the lowland plains of South Island (Te Wai Pounamu) New Zealand (Aoteoroa) contain a ground cover largely consisting of mosses, predominantly Hypnum cupressiforme. There has been no previous study of the role of mosses in this threatened habitat which is currently being restored within a contemporary irrigated and intensively-farmed landscape that may be incompatible with this component of the ecosystem. 2. The aim of the present study was to investigate the influence of moss ground cover on hydrology, nitrogen (N) availability and vascular plant interactions, and in relation to nutrient spillover from adjacent farmland. Experimental work was a combination of glasshouse experiments and field-based studies. 3. Extremes of soil temperature and moisture were found to be mediated by the moss carpet, which also influenced N speciation; available N declined with moss depth. The moss layer decreased the amount of germination and establishment of vascular plants but, in some cases, enhanced their growth. Spillover of mineral nitrogen and phosphate from farmland enhanced invasion of exotic grasses which may have benefited from conditions provided by the moss carpet. 4. Synthesis: We found the moss layer to be crucial to ecosystem functioning in these dry habitats with low nutrient substrate. However, when the moss layer is accompanied by nutrient spillover it has the potential to increase exotic weed encroachment. Our results emphasise the importance of non-vascular plant inclusion in restoration schemes but also highlights the importance of mitigating for nutrient spillover.
The reintroduction of endangered plant species is an essential conservation tool. Reintroductions can fail to create resilient, self-sustaining populations due to a poor understanding of environmental factors that limit or promote plant success. Biotic factors, specifically plant-arthropod interactions, have been shown to affect the establishment of endangered plant populations. Lupinus nipomensis (Nipomo Mesa lupine) is a state of California (California Rare Plant Rank: 1B.1) and federally (65 FR 14888) endangered endemic plant with only one extant population located along the central California coast. How arthropods positively or negatively interact with L. nipomensis is not well known and more information could aid conservation efforts. We conducted arthropod surveys of the entire L. nipomensis extant population in spring 2017. Observed arthropods present on L. nipomensis included 17 families, with a majority of individuals belonging to Thripidae. We did not detect any obvious pollinators of L. nipomensis, providing support for previous studies suggesting this lupine is capable of self-pollinating, and observed several arthropod genera that could potentially impact the reproductive success of L. nipomensis via incidental pollination or plant predation.
The subphylum Myriapoda included four extant classes (Chilopoda, Symphyla, Diplopoda and Pauropoda), but very little work has been done to explore their phylogenetic relationships. Herein, we determined the complete mitochondrial genome of Polydesmus sp. GZCS-2019 (Myriapoda: Polydesmida) and the mitochondrial genomes are circular molecules of 15,036 bp, with all genes encoded on + strand. The A+T content is 66.1%, making the chain asymmetric, and exhibits negative AT-skew (-0.236). Several genes rearrangements were detected and we propose a new rearrangement model: “TD (N\R) L + C” based on the genome-scale duplication + (non-random/random) loss + recombination. Phylogenetic analyses demonstrated that Chilopoda and Symphyla both were monophyletic group, whereas Pauropoda was embedded in Diplopoda to form the Dignatha. Divergence time showed the first split of Myriapoda occurred between the Chilopoda and other classes (Wenlock period of Silurian). We combine phylogenetic analysis, divergence time, and gene arrangement to yield valuable insights into the evolutionary history and classification relationship of Myriapoda and these results support a monophyletic Progoneata and the relationship (Chilopoda + (Symphyla + (Diplopoda + Pauropoda))) within Myriapod. Our results help to better explain the gene rearrangement events of the invertebrate mitogenome and lay the foundation for further phylogenetic study of Myriapoda.
This study compared the microhabitat use, daily activity pattern and diet of Liolaemus etheridgei Laurent 1998 in two Polylepis woodlands: El Simbral (fragmented) and Tuctumpaya (unfragmented), in Arequipa, Southern Peru. In both populations, we did not detect positive selection for any microhabitat; however, the population at El Simbral showed a negative selection for Polylepys trees while the Tuctumpaya population showed negative selection for Polylepis trees and non-thorny bushes. In El Simbral, active individuals were detected between 9:00 and 15:59h, whereas in Tuctumpaya, we detected active individuals from 8:00 to 17:59h. In both populations, observations of active individuals dropped between 11:00 and 11:59h. We recorded 17 and 23 prey categories in the El Simbral and Tuctumpaya populations respectively. The most important animal prey category in each population was found to be Lygaeidae: Hemiptera, and was the only animal prey category that was selected for in El Simbral and Tuctumpaya. In addition, due to the proportions of plant material found, the El Simbral was found to be omnivorous, whereas the Tuctumpaya population was herbivorous. Trophic niche breadth was broader in Tuctumpaya (B_a= 0.202) than the El Simbral (B_a= 0.147) population, despite there being no significant differences in diet (Permanova: F = 1.036, P = 0.409, permutations = 9999), which is coherent with the high value of trophic niche overlap (O_(j,k) = 0.963). Our compiled data reveal that L. etheridgei shows no selection for any of the resources we define in Polylepis woodlands, on the contrary, it selects negatively against Polylepis trees and non-thorny bushes. The daily activity patterns indicate a bimodal pattern with peaks at 9:00-10:59 and 13:00-13:59 h. The diet of L. etheridgei consists mainly of plants (%W: 66.373), and the most important animal prey category is Lygaeidae: Hemiptera (%IRI = 55.3), which is selected positively.
Species traits influence their response to environmental conditions and the match between phenotypes and environment mediates spatial changes in species composition. These trait-environment linkages can be disrupted in human-modified landscapes. Human land-use creates habitat fragments where dispersal limitation or edge effects can exclude species that may otherwise suit a given macro-scale environment. Furthermore, stressful micro-environments in fragments may limit viable trait combinations resulting in stronger trait covariance compared to contiguous forest, especially in harsher macroenvironments. In a wet tropical forest landscape in the Western Ghats Biodiversity Hotspot of peninsular India, I compared fragments with adjacent contiguous forest for signatures of trait-mediated assembly of tree communities along macroenvironmental gradients. Using four key plant traits—seed size, specific leaf area (SLA), wood density, and maximum height—I evaluated changes in trait-mediated abundances and trait covariance across environmental gradients. Trait-mediated abundances primarily changed along the elevation gradient in contiguous forest, smaller-seeded, shorter, thinner-leaved species increased at higher elevations. In fragments, higher SLA species increased in more seasonal climate and decreased with higher precipitation, and larger seeds decreased at warmer sites. However, traits only weakly predicted abundances and only contiguous forests experienced significant compositional change via traits, driven by trait syndromes varying along a composite environmental gradient defined by elevation, water deficit, and soil C:N ratio. Covariance of seed size and maximum height along gradients of precipitation and temperature revealed divergent constraints on viable phenotypes in fragments and contiguous forest. Notably, local biotic conditions (functional diversity) had stronger effects than environment in explaining trait covariance. Overall, the results imply that trait syndromes and trait covariance, rather than single traits, determine the phenotypes best suited to different macroenvironmental conditions and should inform management or restoration goals in fragments.
Although insect herbivores are known to evolve resistance to insecticides through multiple genetic mechanisms, resistance in individual species has been assumed to follow the same mechanism. While both mutations in the target site insensitivity and increased amplification are known to contribute to insecticide resistance, little is known about the degree to which geographic populations of the same species differ at the target site in a response to insecticides. We tested structural (e.g. mutation profiles) and regulatory (e.g. the gene expression of Ldace1 and Ldace2, AChE activity) differences between two populations (Vermont, USA and Belchow, Poland) of the Colorado potato beetle, Leptinotarsa decemlineata in their resistance to two commonly used groups of insecticides, organophosphates, and carbamates. We established that Vermont beetles were more resistant to azinphos-methyl and carbaryl insecticides compared to Belchow beetles, despite a similar frequency of resistance-associated alleles (i.e. S291G) in the Ldace2 gene. However, the Vermont population had two additional amino acid replacements (G192S, F402Y) in the Ldace1 gene, which were absent in the Belchow population. Moreover, the Vermont population showed higher expression of Ldace1 and was less sensitive to AChE inhibition by azinphos methyl oxon than the Belchow population. Therefore, the two populations have evolved different genetic mechanisms to adapt to organophosphate and carbamate insecticides.