Aim Determine seasonal, annual and decadal patterns of abundance in reptile populations and assemblages occupying an isolated urban bushland remnant Location Bold Park (~338 ha), Perth, Southwestern Australia Time period 1986-2021 Major taxa studied: Squamate reptiles Methods Fenced pitfall trapping in four sampling sites representing different habitats and fire history over the primary reptile activity period and 35 consecutive years; trapping regime was modified for the last 28 years. Results The location occurs in one of 35 global biodiversity hotspots and has a Mediterranean climate experiencing a 15% decline from the century average rainfall over the last 50 years. Twenty-nine species were recorded, with 16 captured in 32 or more years and accounting for nearly 97% of all captures; the six most common for 81%. Three taxa became locally extinct. Activity predominates in warmer and dryer months (October to April), peaking in November December. Species richness remained relatively constant between years with around 73% of known taxa captured annually. Assemblage structure didn’t change when analysing presence/absence data but shifted through five statistically significantly assemblages analysing relative abundance data. Over the last 28 years relative abundance was significantly and positively correlated with annual rainfall residuals for the three years preceding annual sampling, resulting in significant changes in total assemblage structure and significantly similar patterns in four sample sites; presence/absence data indicated minor assemblage structure changes. Main conclusions Annual species number remained relatively constant but relative abundance illustrated significant temporal changes in assemblage structure over decades; presence/absence did not. The modeled relationship between relative abundance and annual rainfall residuals for the three years preceding annual sampling is supported by known ecological responses and reptile demographics within this Mediterranean climate. Maintenance of urban biodiversity should consider impacts of a significantly drying climate exacerbating the extinction debt already inherent in isolated bushland populations.
Abiotic and biotic factors structure species assembly in ecosystems both horizontally and vertically. However, the way community composition changes along comparable horizontal and vertical distances in complex three-dimensional habitats, and the factors driving these patterns, remain poorly understood. By sampling ant assemblages at comparable vertical and horizontal spatial scales in a tropical rain forest, we compared observed patterns with those predicted according to environmental filtering by microclimate and microhabitat structure. We found that although dissimilarity between ant assemblages increased with vertical distance, the dissimilarity was higher horizontally but was independent of distance. The pronounced horizontal and vertical structuring of ant assemblages across short distances is likely explained by a combination of microclimate and microhabitat connectivity. Our results demonstrate the importance of considering three-dimensional spatial variation in local assemblages and reveal how highly diverse communities can be supported by complex habitats.
Understanding the extent to which predators engage in active search for prey versus incidentally encountering them is important because active search can exert a stabilizing force on prey populations by alleviating predation pressure on low-density prey and increasing it for high-density prey. Parturition of many large herbivores occurs during a short and predictable temporal window in which young are highly vulnerable to predation. Our study aims to determine how a suite of carnivores responds to the seasonal pulse of newborn ungulates using contemporaneous GPS locations of four species of predators and two species of prey. We used step-selection functions to assess whether coyotes, cougars, black bears, and bobcats actively searched for parturient females in a low-density population of mule deer and a high-density population of elk. We then assessed whether searching carnivores shifted their habitat use toward areas exhibiting a high probability of encountering neonates. None of the four carnivore species encountered parturient mule deer more often than expected by chance suggesting that predation of young resulted from incidental encounters. By contrast, we determined that cougar and male bear movements positioned them in proximity of parturient elk more often than expected by chance which is evidence of searching behavior. Although both male bears and cougars searched for neonates, only male bears used elk parturition habitat in a way that dynamically tracked the phenology of the elk birth pulse suggesting that maximizing encounters with juvenile elk was a motivation when selecting resources. Our results support the existence of a stabilizing mechanism to prey populations through active search behavior by predators because carnivores in our study searched for the high-density prey species (elk) but ignored the low-density species (mule deer). We conclude that prey density must be high enough to warrant active search, and that there is high interspecific and intersexual variability in foraging strategies among large mammalian predators and their prey.
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 rapid urbanization has caused changes in climate and environment and threatened the ecosystem with multiple risks. The ecological service capacity has shown a downward trend accordingly. It is significant to explore the spatio-temporal evolution of land use and ecological service value in mountainous counties at small scales, as it coordinates economic growth and ecological protection, and promotes sustainable and high-quality development. Based on the SD-PLUS model, taking Qianshan city as an example, the study simulated three scenarios of land use change: ecological protection, coordinated development, and economic priority, and studied the impacts of land use change on the value of ecosystem services. Results showed that: ① Under the three scenarios, the construction land in the study area increased significantly, the forest and water area have a decreasing trend, and the scale of gardens has partly increased. ② Construction land expands in clusters in the urban built-up areas and dots in mountainous areas; land use changes are primarily affected by roads, followed by areas where artificial facilities are relatively sparse, and DEM has the greatest impact on land use changes. ③ The overall ecosystem service value shows a downward trend, with the comprehensive coordination type dropping the least (8.79%). The value distribution changes little at space scale, and different regions demonstrate different degrees of changes. From the perspective of value type, the service values of climate regulation and water conservation are significantly reduced, while that of food production is relatively stable; and from the perspective of various lands with their ecological service values, cultivated land and forest remain stable. The study results can provide technical ideas for the coordinated economic development and ecological protection of mountainous cities, and boost the implementation of green development.
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.