First experimental evidence for active farming in ambrosia beetles and strong heredity of garden microbiomes

Fungal cultivation is a defining feature for advanced agriculture in fungus-farming ants and termites. In a third supposedly fungus-farming group, wood-colonizing ambrosia beetles, an experimental proof for the effectiveness of beetle activity for selective promotion of their food fungi over others is lacking and farming has only been assumed based on observations of social and hygienic behaviours. Here, we experimentally removed mothers and their offspring from young nests of the fruit-tree pinhole borer, Xyleborinus saxesenii. By amplicon sequencing of bacterial and fungal communities of nests with and without beetles we could show that beetles are indeed able to actively shift symbiont communities. Although being consumed, the Raffaelea food fungi were more abundant when beetles were present while a weed fungus (Chaetomium sp.) as well as overall bacterial diversity were reduced in comparison to nests without beetles. Core symbiont communities were generally of low diversity and there were strong signs for vertical transmission not only for the cultivars, but also for secondary symbionts. Our findings verify the existence of active farming, even though the exact mechanisms underlying the selective promotion and/or suppression of symbionts need further investigation.

A Global review of cumulative effects assessments of disturbances on forest ecosystems

This paper reviews trends in the academic literature on cumulative effects assessment (CEA) of disturbance on forest ecosystems to advance research in the broader context of impact assessments. Disturbance is any distinct spatiotemporal event that disrupts the structure and composition of an ecosystem affecting resource availability. We developed a Python package to automate search term selection, write search strategies, reduce bias and improve the efficient and effective selection of articles from academic databases and grey literature. We identified 148 peer-reviewed literature published between 1986 and 2022 and conducted an inductive and deductive thematic analysis of the results. Our findings revealed that CEA studies are concentrated in the global north, with most publications from authors affiliated with government agencies in the USA and Canada. Methodological and analytical approaches are less interdisciplinary but mainly quantitative and expert-driven, involving modeling the impacts of disturbances on biophysical valued components. Furthermore, the assessment of socioeconomic valued components, including the effects of disturbance on Indigenous wellbeing connected to forests, has received less attention. Even though there is a high preference for regional assessment, challenges with data access, quality, and analysis, especially baseline data over long periods, are hampering effective CEA. Few articles examined CEA - policy/management nexus. Of the few studies, challenges such as the inadequate implementation of CEA mitigation strategies due to policy drawbacks and resource constraints, the high cost of monitoring multiple indicators, and poor connections between scenarios/modeling and management actions were paramount. Future CEA research is needed to broaden our understanding of how multiple disturbance affects forests in the global south and coupled social and ecological systems and their implications for sustainable forest management.

GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species

Background

Many wild species have suffered drastic population size declines over the past centuries, which have led to ‘genomic erosion’ processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates of modern-day populations often lack concordance with dwindling population sizes and conservation status of threatened species. One way to directly quantify the genomic consequences of population declines is to compare genome-wide data from pre-decline museum samples and modern samples. However, doing so requires computational data processing and analysis tools specifically adapted to comparative analyses of degraded, ancient or historical, DNA data with modern DNA data as well as personnel trained to perform such analyses.

Results

Here, we present a highly flexible, scalable, and modular pipeline to compare patterns of genomic erosion using samples from disparate time periods. The GenErode pipeline uses state-of-the-art bioinformatics tools to simultaneously process whole-genome re-sequencing data from ancient/historical and modern samples, and to produce comparable estimates of several genomic erosion indices. No programming knowledge is required to run the pipeline and all bioinformatic steps are well-documented, making the pipeline accessible to users with different backgrounds. GenErode is written in Snakemake and Python3 and uses Conda and Singularity containers to achieve reproducibility on high-performance compute clusters. The source code is freely available on GitHub (https://github.com/NBISweden/GenErode).

Conclusions

GenErode is a user-friendly and reproducible pipeline that enables the standardization of genomic erosion indices from temporally sampled whole genome re-sequencing data.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12859-022-04757-0.

Two Mechanisms Drive Changes in Boreal Peatland Photosynthesis Following Long-Term Water Level Drawdown: Species Turnover and Altered Photosynthetic Capacity

Climate change and the related increases in evapotranspiration threaten to make northern peatlands drier. The carbon sink function in peatlands is based on the delicate balance between the photosynthesis and decomposition. However, little is known about how existing and invading plant species will photosynthesize under drier conditions. The aim of this study is to quantify the long-term consequences of climate change-induced drying for peatland photosynthesis in the level of individual species and vegetation community. We measured the species-level photosynthesis of vascular plants and mosses characteristic for the three peatland types (rich fen, poor fen, bog) within a 16-year water level drawdown (WLD) experiment. Measurements were made in the laboratory from mesocosms collected from the field within the same day. We applied nonlinear mixed-effects models to test the impact of WLD on hyperbolic photosynthetic light response curve parameters. The model was then used to upscale photosynthesis to site-level. WLD impacted site-level photosynthesis through two mechanisms: species turnover and changes in species-level photosynthesis rate. The rich fen was the most sensitive and underwent major changes through both mechanisms; the vascular plant community shifted to woody plant dominance with higher rate of photosynthesis than the pre-treatment vegetation, and the rate of species-level photosynthesis increased significantly. The bog had a stable plant community with little change in photosynthesis, while the poor fen was an intermediate of the three peatland types. Our results suggest that vascular plants are the main drivers of site-level productivity changes, while mosses are more resistant to change. The change seems proportional to the availability of mineral nutrients, with higher nutrient status supporting vascular plant expansion.

Predator cue-induced plasticity of morphology and behavior in planthoppers facilitate the survival from predation

Predators can induce phenotypic plasticity in prey through selection driven by predation risk. However, defense plasticity is rarely reported in insects, let alone trans-generational plasticity, meaning the mechanisms underlying plasticity, how it impacts ecosystem evolution and how it might be exploited in pest control are poorly understood. Here we examine the morphological plasticity of small brown planthoppers (SBPHs), Laodelphax striatellus, elicited by caged predators, Paederus fuscipes in the parent or F1 generation and reveal the risk cues mediating these effects. We also uncover the survival outcomes in SBPHs with predator-induced defensive morphological traits by examining their survival probability and behavioral plasticity. Results showed that caged predators or predator odor cue gave rise to a higher proportion of long-winged, female SBPHs in the parent and F1 generations, but the proportion of males and their wing length were unaffected. The visual cue from predators elicited weaker effects. Surprisingly, we discovered these long-winged forms suffered a lower predation rate when attacked by P. fuscipes, owing to an enhanced agility level. Our results suggest the within- and trans-generational plasticity of induced defenses may cause profound effects on SBPH population dynamics and prey-predator interaction. Understanding this interaction and its underlying mechanisms illuminates important aspects of ecosystem evolution and helps predict pest dispersal or migration, which in turn may be exploited for pest control.

Prevalence and patterns of scavenging by brown bears (Ursus arctos) on salmon (Oncorhynchus spp.) carcasses

Scavenging, an underappreciated mechanism of prey consumption for many predators, can contribute substantially to nutritional intake. Facultative scavengers such as brown bears (Ursus arctos Linnaeus, 1758) may both kill and scavenge Pacific salmon (genus Oncorhynchus Suckley, 1861), though the extent of scavenging and factors affecting this behavior are unclear. We tagged 899 sockeye salmon (Oncorhynchus nerka (Walbaum in Artedi, 1792)) carcasses and placed them on streambanks over 5 years at multiple sites in southwestern Alaska (USA) where brown bears annually prey on spawning sockeye salmon. Examination of carcasses revealed overall scavenging rates of 15% after 1 day and 54% after 3 days. Scavenging rate varied by site and year and increased throughout the salmon run. Contrary to predictions, scavenging was more frequent in senescent or bear-killed carcasses than ripe carcasses. Carcass consumption ranged from minimal to almost complete; body and brain tissues were most frequently consumed after 3 days (68% and 63% of carcasses, respectively). We also documented secondary scavenging (i.e., tissue consumption on two separate events) and delayed scavenging (i.e., scavenging observed after 3 days but not 1 day). Taken together, the results indicated that scavenging in these streams contributes significantly to total consumption of salmon by bears, with ramifications for other components of these salmon-dependent ecosystems.

No evidence for individual recognition in threespine or ninespine sticklebacks (Gasterosteus aculeatus or Pungitius pungitius)

Recognition plays an important role in the formation and organization of animal groups. Many animals are capable of class-level recognition, discriminating, for example, on the basis of species, kinship or familiarity. Individual recognition requires that animals recognize distinct cues, and learn to associate these with the specific individual from which they are derived. In this study, we asked whether sticklebacks (Gasterosteus aculeatus and Pungitius pungitius) were capable of learning to recognize individual conspecifics. We have used these fish as model organisms for studying selective social learning, and demonstrating a capacity for individual recognition in these species would provide an exciting opportunity for studying how biases for copying specific individuals shape the dynamics of information transmission. To test for individual recognition, we trained subjects to associate green illumination with the provision of a food reward close to one of two conspecifics, and, for comparison, one of two physical landmarks. Both species were capable of recognizing the rewarded landmark, but neither showed a preference for associating with the rewarded conspecific. Our study provides no evidence for individual recognition in either species. We speculate that the fission-fusion structure of their social groups may not favour a capacity for individual recognition.