The subfamily Typhlocybinae is a ubiquitous, highly diverse group of mostly tiny, delicate leafhoppers. The tribal classification has long been controversial and phylogenetic methods have only recently begun to test the phylogenetic status and relationships of tribes. To shed light on the evolution of Typhlocybinae, we performed phylogenetic analyses based on 28 newly sequenced and 19 previously sequenced mitochondrial genomes representing all currently recognized tribes. The results support the monophyly of the subfamily and its sister group relationship to Mileewinae. The tribe Zyginellini is polyphyletic with some included genera derived independently within Typhlocybini. Ancestral character state reconstruction suggests that some morphological characters traditionally considered important for diagnosing tribes (presence/absence of ocelli, development of hind wing submarginal vein) are homoplastic. Divergence time estimates indicate that the subfamily arose during the Middle Cretaceous and that the extant tribes arose during the Late Cretaceous. Phylogenetic results support establishment of a new genus, Subtilissimia Yan & Yang gen. nov., with two new species, Subtilissimia fulva Yan & Yang sp. nov. and Subtilissimia pellicula Yan & Yang sp. nov. (Typhlocybinae: Typhlocybini); but indicate that two previously recognized species of Farynala distinguished only by the direction of curvature of the processes of the aedeagus are synonyms, i.e., Farynala dextra Yan & Yang, 2017 equals Farynala sinistra Yan & Yang, 2017 syn. nov. A key to tribes of Typhlocybinae is provided.
Gobbling activity of Eastern wild turkeys (Meleagris gallopavo silvestris; hereafter, turkeys) has been widely studied, focusing on drivers of daily variation. Weather variables are widely believed to influence gobbling activity, but results across studies are contradictory and often equivocal, leading to uncertainty in the relative contribution of weather variables to daily fluctuations in gobbling activity. Previous works relied on road-based auditory surveys to collect gobbling data which limits data consistency, duration, and quantity due to logistical difficulties associated with human observers and restricted sampling frames. Development of new methods using autonomous recording units (ARUs) allows researchers to collect continuous data in more locations for longer periods of time, providing the opportunity to delve into factors influencing daily gobbling activity. We used ARUs from 1 March to 31 May to detail gobbling activity across multiple study sites in the southeastern United States during 2014 – 2018. We used state-space modeling to investigate the effects of weather variables on daily gobbling activity. Our findings suggest rainfall, greater wind speeds, and greater temperatures negatively affected gobbling activity, whereas increasing barometric pressure positively affected gobbling activity. Therefore, when using daily gobbling activity to make inferences relative to gobbling chronology, reproductive phenology, and hunting season frameworks stakeholders should recognize and consider the potential influences of extended periods of inclement weather.
The Tanzania-Zambia (TANZAM) Highway traversing Mikumi National Park (MINAPA) has been a concern for wildlife managers since it was first paved in 1973-74. After its upgrade in 1989-90, researchers have documented increasing traffic resulting in considerable animal injuries and mortalities. Yellow baboons in MINAPA are known to use the road as their bridge to and from foraging areas, therefore in addition to the risk of mortality; road use could potentially have significant influence on their feeding behaviour. However, knowledge on the influences of the TANZAM highway in the feeding behaviour of the baboons is sparse. Using focal animal sampling techniques, we collected data on feeding and foraging behaviour of two habituated troops of yellow baboons to examine to what extent the TANZAM highway is important in their feeding and foraging behaviour. Results showed that in relation to habitat availability, visitation to habitat types reflect actual habitat choice of baboons. In general, baboons less frequently visit and spent less time in the highway compared to natural habitats. Whenever they were on the highway, adult females and subadult males engage more into feeding, resting and socializing, while adult males were more vigilant. The major dietary compositions were fruits, seeds, leaves, sap and invertebrates, almost exclusively collected from natural habitats, foods from the highway were opportunistically consumed. This study provides empirical evidence and concludes that yellow baboons do not directly depend on the highway for food, rather they use the TANZAM highway as normal part of their home range. The TANZAM highway is used because it improves visibility and reduces the perceived predation risk compared to natural habitats. However, its location near sleeping sites may have significant impact on baboons’ activity budget. With these findings, we recommend strict implementation of rules against park littering and animal feeding in protected areas traversed by highways.
Understanding the consequences of human induced translocations on natural populations requires genetic monitoring. Salmonid fishes represent a group of species experiencing several such large-scale perturbations expected to affect microevolutionary processes. Here, two genetically separate brown trout populations with divergent life history traits are studied following their release into waters previously void of trout. We use a pooled sequencing approach to explore the genomic characteristics of the released stocks and of populations established in the wild in two lakes down-stream of the release site 30 years (4-5 generations) later. While most of the differences (FST=0.16) between the released stocks can be attributed to drift, we identify putatively adaptive differences between them in genes involved in immunity, hearing, skin and muscle texture. Higher levels of genome-wide diversity in established populations compared to released stocks suggest extensive hybridization between stocks. However, released stocks are unequally represented in the established populations, with one stock mainly contributing to the lake closest to the release site, and the other dominating the lake further downstream. We also identify genomic regions putatively under directional selection in the new environment, where genes from one of the released populations, governing metabolism, appear advantageous. Our results demonstrate that hybridization, establishment, and adaptation can be rapid after release into novel environments. We show that such ongoing processes, important for conservation and management, are possible to monitor over contemporary time scales even for a species with relatively small local effective population sizes and a large, complex genome.
Recent findings suggest that immune functions do not unidirectionally deteriorate with age but that a potentially adaptive remodelling where functions of the immune system get down regulated while others get upregulated with age could also occur. Scarce in wild populations, longitudinal studies are yet necessary to properly understand the patterns and consequences of age variations of the immune system in the wild. In the meanwhile, it is challenging to understand if the observed variations in immune parameters with age are due to changes at the within-individual level or to selective (dis)appearance of individuals with peculiar immune phenotypes. Thanks to a long-term and longitudinal monitoring of a wild population of Alpine marmots, we aimed to understand within- and between-individual variation in the immune phenotype with age, in order to improve our knowledge about the occurrence and the evolutionary consequence of such age-variations in the wild. To do so, we recorded the age-specific leukocyte concentration and profile in repeatedly sampled dominant individuals. We then tested whether the potential changes with age were more likely due to within-individual variations and/or selective (dis)appearance. Finally, we investigated if the leukocyte concentration and profiles were correlated to the probability of death at a given age. The leukocyte concentration was stable with age, but the lymphocyte count decreased, while the neutrophil count increased, over the course of an individual’s life. Moreover, between individuals of the same age, individuals with fewer lymphocytes but more neutrophils were more likely to die. Therefore, selective disappearance seems to play an important role in the age variations of the immune parameters in this population. Further investigations linking age variations in immune phenotype to individual fitness are needed to understand whether remodelling of the immune system with age could or could not be adaptive.
Since water deficit (WD) and ultraviolet radiation (UV) trigger similar protective mechanisms in plants, we tested the hypothesis that UV modulates grassland acclimation to WD, mainly through changes in the root/shoot (R/S) ratio, enhances the ability of grassland to acquire water from the soil and hence affects its productivity. We also tested the potential of spectral reflectance and thermal imaging for monitoring the impacts of WD and UV on grassland production parameters. The experimental plots were manipulated by lamellar shelters allowing precipitation to pass through or to exclude it. The lamellas were either transmitting or blocking the UV. The results show that WD resulted in a significant decrease in above-gound biomass (AB). In contrast, below-ground biomass (BB), R/S ratio and total biomass (TB) increased significantly in response to WD, especially in UV exclusion treatment. UV exposure had a significant effect on AB and BB, but only in the last year of the experiment. The differences in the effect of WD between years show that the effect of precipitation removal is largely influenced by the potential evapotranspiration (PET) in a given year and hence mainly by air temperatures, while the resulting effect on production parameters is best correlated with the water balance given by the difference between precipitation and PET. Canopy temperature and selected spectral reflectance indices showed a significant response to WD and also significant relationships with morphological (AB, R/S) and biochemical (C/N ratio) parameters. In particular, the vegetation indices NDVI and RDVI provided the best correlations of biomass changes caused by WD and thus the highest potential to remotely sens drought effects on terrestrial vegetation.
Species-level taxonomy is derived from methodological sources (data and techniques) that assess the existence of spatio-temporal evolutionary lineages via various species concepts. These concepts determine if observed lineages are independent given a particular methodology supposedly connected to ontology, which relates the metaphysical concept to what “kind” of thing a species is. Often, species concepts fail to link methodology and practice back to ontology. This lack of coherence is in part responsible for the persistence of the rank of subspecies, which in modern usage often functions as a placeholder between the evolutionary events of divergence or collapse. Thus, prospective events like lineage merger or collapse determine if a subspecies is subsumed into an existing species, or achieves species rank given unknowable future information. This is conditioned on evidence that the lineage already has a detectably distinct evolutionary history. Ranking these lineages as subspecies seems attractive given the observation that many lineages do not exhibit intrinsic reproductive isolation. We argue that the use of subspecies is indefensible on philosophical and empirical grounds. Ontologically, the rank of subspecies is either identical to that of species or undefined in the context of evolutionary lineages representing spatio-temporally defined individuals. Some species concepts more inclined to consider subspecies, like the Biological Species Concept, are disconnected from ontology and do not consider genealogical history. Even if ontology is ignored, methods addressing reproductive isolation are often indirect and fail to capture the range of scenarios linking gene flow to species identity over space and time. The use of subspecies and reliance on reproductive isolation as a basis for an operational species concept can also conflict with ethical issues governing the protection of species. We provide a way forward for recognizing and naming species that links theoretical and operational species concepts regardless of the magnitude of reproductive isolation.
Wild bees form diverse communities that pollinate plants in both native and agricultural ecosystems making them both ecologically and economically important. The growing evidence of bee declines has sparked increased interest in monitoring bee community and population dynamics using standardized methods. Here, we studied the dynamics of bee biodiversity within and across years by monitoring wild bees adjacent to four apple orchard locations in Southern Pennsylvania, USA. We collected bees using passive Blue Vane traps continuously from April to October for six years amassing over 26,000 bees representing 144 species. We quantified total abundance, richness, diversity, composition, and phylogenetic structure. There were large seasonal changes in all measures of biodiversity with month explaining an average of 72% of the variation in our models. Changes over time were less dramatic with years explaining an average of 44% of the variation in biodiversity metrics. We found declines in all measures of biodiversity especially in the last 3 years. Analyses of population trends over time for the 40 most abundant species indicate that about one third of species showed at least some evidence for declines in abundance. Bee family explained variation in species-level seasonal patterns but we found no consistent family-level patterns in declines, though bumble bees and sweat bees were groups that declined the most. Overall, our results show that season-wide standardized sampling across multiple years can reveal nuanced patterns in bee biodiversity, phenological patterns of bees, and population trends over time of many co-occurring species. These datasets could be used to quantify the relative effects that different aspects of environmental change have on bee communities and to help prioritize conservation efforts.
The response of communities to climate change is expected to vary among feeding guilds. To evaluate the response of guilds to environmental factors without considering the taxonomic specificities, it is useful to examine Aculeata bees and wasps, which consist of closely related taxa including different guilds, pollinators, predators, and parasitoids. In this study, we evaluated changes in species diversity (SD) and functional traits of each feeding guild along an elevational gradient in a boreal forest in northern Japan. We used yellow pan traps to collect Aculeata bees and wasps at 200–1600 m above sea level. We investigated six functional traits (trophic level, flight duration, body size, elevational range, nesting position, and soil dependency) and the horizontal distribution of the species. The SD of all Aculeata predators and parasitoids decreased with an increase in elevation; however, the SD of pollinators did not show any specific trend. Although the functional trait composition of all Aculeata species did not show any trend, that of each feeding guild responded to elevation in different ways. Pollinators increased in body size and showed a decrease in flight duration with increasing elevation, suggesting that tolerance and seasonal escape from physical stress at high elevations are important for shaping pollinator communities. Predators showed increased elevational range and above-ground nesting species with increasing elevation, suggesting that the ability to live in a wider range of environments and avoid unsuitable soil environments at high elevations might be important. Parasitoids changed their hosts and variable traits with increasing elevation, suggesting that brood parasitoids have difficulty in surviving at high elevation. The traits for each guild responded in different ways, even if they were dominated by the same environmental factors. Differences in the response of functional traits would produce different patterns of community formation in different guilds during further climate change.
Soil microorganisms are crucial contributors to the function of permafrost ecosystems, as well as the regulation of biogeochemical cycles. However, little is known about the distribution patterns and drivers of high-latitude permafrost microbial communities subject to climate change and human activities. In this study, the vertical distribution patterns of soil bacterial communities in the Greater Khingan Mountain permafrost region were systematically analyzed via Illumina Miseq high-throughput sequencing. Bacterial alpha diversity varied significantly at different soil depths, and the bacterial diversity and richness in the active layer were significantly higher than in the permafrost layer. The relative abundance of the dominant phyla Chloroflexi (17.92%–52.79%) and Actinobacteria (6.34%–34.52%) was significantly higher in the permafrost layer than in the active layer, whereas that of Acidobacteria (4.98%–38.82%) exhibited the opposite trend, and the abundance of Proteobacteria (2.49%–22.51%) generally decreased with depth. More importantly, the abundance of microorganisms linked to human infectious diseases was significantly higher in the permafrost layer according to Tax4Fun prediction analysis. Redundancy analysis (RDA) showed that NH4+-N, TOC and TP were major factors affecting the bacterial community composition. Collectively, our findings provide insights into the soil bacteria at different depths in high-latitude permafrost regions, as well as their vertical distribution patterns and major environmental drivers, which is key to grasping the response of cold region ecosystem processes to global climate changes.
Association is the basic unit of plant community classification. Exploring the distribution of plant associations can help improve the understanding of biodiversity conservation. Different associations depend on different habitats. Studying the association level is significant for ecological restoration, regional ecological protection, regulating the ecological balance, and maintaining biodiversity. However, previous studies have focused only on the suitable distribution areas of species and not on the distribution of plant associations. Larix gmelinii is a sensitive and abundant species spread in the southern margin of Eurasian boreal forests, and its distribution is closely related to permafrost. In this study, 420 original plots of L. gmelinii forests were investigated. We used Maxent model and ArcGIS software to project the potential geographical distribution of L. gmelinii associations in the future (by 2050 and 2070) according to the climate scenarios RCP 2.6, RCP 4.5, and RCP 8.5. The causes for the changes in spatial distribution were analyzed using multinomial logistic regression analysis. The results revealed that temperature is the most important factor affecting the distribution of L. gmelinii forests and most of its associations under different climate scenarios. Further, the suitable areas for each association type are shrinking by varying degrees, especially due to habitat loss at high altitudes in special terrains. For different L. gmelinii associations, management measures should also be different based on the different site conditions, composition structure, growth, development, and renewal succession trends. Furthermore, subsequent research should consider data on biological factors to obtain more accurate prediction results.
The horned gall aphid Schlechtendalia chinensis, is an economically important insect that induces galls valuable for medicinal and chemical industries. S. chinensis manipulates its host plant to form well-organized horned galls during feeding. So far, more than twenty aphid genomes have been reported; however, all of those are derived from free-living aphids. Here we generated a high-quality genome assembly of S. chinensis, representing the first genome sequence of a galling aphid. The final genome assembly was 280.43 Mb, with 97% of the assembled sequences anchored into thirteen chromosomes. S. chinensis presents the smallest aphid genome size among available aphid genomes to date. The contig and scaffold N50 values were 3.39 Mb and 20.58 Mb, respectively. The assembly included 96.4% of conserved arthropod and 97.8% of conserved Hemiptera single-copy orthologous genes based on BUSCO analysis. A total of 13,437 protein-coding genes were predicted. Phylogenomic analysis showed that S. chinensis formed a single clade between the Eriosoma lanigerum clade and the Aphidini+Macrosiphini aphid clades. In addition, salivary proteins were found to be differentially expressed when S. chinensis underwent host alternation, indicating their potential roles in gall formation and plant defense suppression. A total of 36 cytochrome P450 genes were identified in S. chinensis, considerably fewer compared to other aphids, probably due to its small host plant range. The high-quality S. chinensis genome assembly and annotation provide an essential genetic background for future studies to reveal the mechanism of gall formation and to explore the interaction between aphids and their host plants.
Metabarcoding has improved the way we understand plants within our environment, from their ecology and conservation to invasive species management. The notion of identifying plant taxa within environmental samples relies on the ability to match unknown sequences to known reference libraries. Without comprehensive reference databases, species can go undetected or be incorrectly assigned, leading to false positive and negative detections. To improve our ability to generate reference sequence databases we developed a targeted capture approach using the OZBaits_CP V1.0 set, designed to capture chloroplast gene regions across the entirety of flowering plant diversity. We focused on generating a reference database for coastal temperate plant species given the lack of reference sequences for these taxa. Our approach was successful across all specimens with a target gene recovery rate of 92% which was achieved in a single assay (i.e., samples were pooled), thus making this approach much faster and more efficient than standard barcoding. Further testing of this database highlighted 80% of all samples could be discriminated to family level across all gene regions with some genes achieving greater resolution than others – which was also dependant on the taxon of interest. Thus, we demonstrate the importance of generating reference sequences across multiple chloroplast gene regions as no single loci is sufficient to discriminate across all plant groups. The targeted capture approach outlined in this study provides a way forward to achieve this.
In long-lived species, reproductive skipping is a common strategy whereby sexually mature animals skip a breeding season, potentially reducing population growth. This may be an adaptive decision to protect survival, or a non-adaptive decision driven by individual-specific constraints. Understanding the presence and drivers of this behaviour is key to effective population management, yet in many species such as the endangered African penguin (Spheniscus demersus), these factors remain unknown. This study uses multistate mark-recapture methods to estimate African penguin survival and breeding probabilities at two colonies between 2013 and 2020. Overall, survival was higher at Stony Point (0.82) than Robben Island (0.77). Inter-colony differences were linked to food availability; under decreasing sardine (Sardinops sagax) abundance, survival decreased at Robben Island and increased at Stony Point. Additionally, reproductive skipping was evident across both colonies; at Robben Island ~22% of breeding individuals skipped reproduction each year, versus ~10% at Stony Point. Penguins skipping reproduction had a lower probability of future breeding than breeding individuals; this lack of adaptive benefit suggests reproductive skipping is driven by individual-specific constraints. Lower survival and breeding propensity at Robben Island places this colony in greater need of conservation action. However, further research on the drivers of inter-colony differences is needed.
Ecological restoration of former agricultural land can improve soil condition, recover native vegetation, and provide fauna habitat. However, restoration benefits are often associated with time lags, as many attributes, such as leaf litter and coarse woody debris, need time to accumulate. Here we experimentally tested whether adding fine and coarse woody debris to a decade-old restoration sites can accelerate restoration benefits. We used a Multi-site Before-After / Control-Impact design to test the effects on 30 response variables over a period of two years, including those describing soil physical and biochemical properties, herbaceous vegetation and ant communities. We analysed the data using linear mixed-effect models and perMANOVAs. Of the 30 response variables, a significant effect of mulch or log additions was found for just four variables: volumetric water content, decomposition of tea leaves, native herbaceous species cover and species richness of opportunistic ants. Mulch addition had a positive effect on soil moisture when compared to controls but suppressed growth of native (but not exotic) herbaceous plants. Whilst other soil properties such as organic matter and dissolved organic carbon showed a positive response to mulch addition, the effect was not statistically significant. On plots with log additions, decomposition rates of tea leaves decreased, and species richness of opportunistic ants increased. However, we found no effect on total species richness and abundance of other ant functional groups. The benefit of mulch to soil moisture was offset by its disbenefit to native herbs in our study. Logs increased species richness of opportunistic ants, but given time, may provide habitat for cryptic species. Indeed, benefits to other soil biophysical properties, vegetation and ant fauna may require longer timeframes to be detected. Further research is needed to determine whether the type, quantity and context of mulch and log additions may improve restoration outcomes.
Environmental temperature is a key driver of malaria transmission dynamics. Using detailed temperature records from four sites (1800-3200m) in the western Himalaya, we model how temperature regulates parasite development rate (the inverse of the extrinsic incubation period, EIP) in the wild. Using a Briére parametrization of the EIP, combined with Bayesian parameter inference, we study the thermal limits of transmission for avian (P. relictum) and human Plasmodium parasites (P. vivax and P. falciparum) as well as for two malaria-like avian parasites, Haemoproteus and Leucocytozoon. We demonstrate that temperature conditions can substantially alter the incubation period of parasites at high elevation sites (2600-3200m) leading to restricted parasite development or long transmission windows. We then compare estimates of EIP based on measures of mean temperature versus hourly temperatures to show that EIP days vary in cold versus warm environments. We found that human Plasmodium parasites experience a limited transmission window at 2600m. In contrast, for avian Plasmodium transmission was not possible between September to March at 2600m. In addition, temperature conditions suitable for both Haemoproteus and Leucocytozoon transmission were obtained from June to August and in April, at 2600m. Finally, we use temperature projections from a suite of climate models to predict that by 2040, high elevation sites (~ 2600 m) will have a temperature range conducive for malaria transmission, albeit with a limited transmission window. Our study highlights the importance of accounting for fine-scale thermal effects in the expansion of the range of the malaria parasite with global climate change.
Climate change and fisheries exploitation are dramatically changing the species composition, abundances, and size spectra of fish communities. We explore whether variation in abundance-size spectra, a widely studied ecosystem feature, is influenced by a critical parameter thought to govern the shape of size-structured ecosystems—the relationship between the sizes of predators and their prey (predator-prey mass ratios, or PPMRs). PPMR estimates are lacking for vast numbers of fish species, including at the broader trophic guild scale. Using measurements of 8,128 prey items in gut contents of 97 reef fish species, we established PPMRs for four major trophic guilds (piscivores, invertivores, planktivores and herbivores) using linear mixed effects models. To assess theoretical predictions that higher mean community-level PPMR leads to shallower size spectrum slopes, we compared observations of mean community-level PPMR with size spectrum slopes for coastal reef sites distributed around Australia. PPMRs of individual fishes were remarkably high (median ~71,000), with significant variation between different trophic guilds (~890 for piscivores; ~83,000 for planktivores), and ~8,700 for whole communities. Community-level PPMRs were positively related to size spectrum slopes, broadly consistent with theory, however, this pattern was also influenced by the latitudinal temperature gradient. Tropical reefs showed a stronger relationship between community-level PPMRs and community size spectrum slopes than temperate reefs. The extent that these patterns apply outside Australia, and consequences for community structure and dynamics, are key areas for future investigation.
The South American temperate forests have been subjected to drastic past topographic and climatic changes during the Pliocene – Pleistocene linked to Andean orogeny and glacial cycles. These changes are common drivers of genetic structure and adaptation process. Embothrium coccineum, a member of the Proteaceae family and an emblematic tree of the South American temperate forest with a distribution spanning 20° of latitude, has been strongly affected by these topographic and climatic changes. Previous studies have shown that the species presents a marked genetic structure with distinct ecotypes described; yet, little is known about their adaptive genetic responses. The main goal of this study was to investigate the effects of historical and contemporary landscape features affecting the genetic diversity and connectivity of E. coccineum throughout its natural distribution. Using more than 2000 SNPs, two genetic groups (North and Center-South) that have diverged some 2.8 million years ago were observed. The level of genetic structure was higher between populations within the North genetic group than within the Center-South group. We propose that these contrasting patterns of genetic structure are related to differences in pollinator’s assemblage and evolutionary histories between genetic groups. Moreover, we observed the existence a strong patter of isolation by environment in E. coccineum, suggesting that selection could have leaded to adaptive divergence among localities. We propose that, within the Chilean temperate forest, the patterns of genetic variation in E. coccineum reflect both a Quaternary phylogenetic imprint and the impact of selection to the strong environmental gradient.