Ecological specialization and niche overlap of subterranean rodents inferred from DNA metabarcoding diet analysis

Is the diet cyclic phase-dependent in boreal vole populations?

Herbivorous rodents in boreal, alpine and arctic ecosystems are renowned for their multi-annual population cycles. Researchers have hypothesised that these cycles may result from herbivore-plant interactions in various ways. For instance, if the biomass of preferred food plants is reduced after a peak phase of a cycle, rodent diets can be expected to become dominated by less preferred food plants, leading the population to a crash. It could also be expected that the taxonomic diversity of rodent diets increases from the peak to the crash phase of a cycle. The present study is the first to use DNA metabarcoding to quantify the diets of two functionally important boreal rodent species (bank vole and tundra vole) to assess whether their diet changed systematically in the expected cyclic phase-dependent manner. We found the taxonomic diet spectrum broad in both vole species but with little interspecific overlap. There was no evidence of systematic shifts in diet diversity metrics between the phases of the population cycle in either species. While both species' diet composition changed moderately between cycle phases and seasons, these changes were small compared to other sources of diet variation-especially differences between individuals. Thus, the variation in diet that could be attributed to cyclic phases is marginal relative to the overall diet flexibility. Based on general consumer-resource theory, we suggest that the broad diets with little interspecific overlap render it unlikely that herbivore-plant interactions generate their synchronous population cycles. We propose that determining dietary niche width should be the first step in scientific inquiries about the role of herbivore-plant interactions in cyclic vole populations.

Small rodent population cycles and plants - after 70 years, where do we go?

Small rodent population cycles characterise northern ecosystems, and the cause of these cycles has been a long-lasting central topic in ecology, with trophic interactions currently considered the most plausible cause. While some researchers have rejected plant-herbivore interactions as a cause of rodent cycles, others have continued to research their potential roles. Here, we present an overview of whether plants can cause rodent population cycles, dividing this idea into four different hypotheses with different pathways of plant impacts and related assumptions. Our systematic review of the existing literature identified 238 studies from 150 publications. This evidence base covered studies from the temperate biome to the tundra, but the studies were scattered across study systems and only a few specific topics were addressed in a replicated manner. Quantitative effects of rodents on vegetation was the best studied topic, and our evidence base suggests such that such effects may be most pronounced in winter. However, the regrowth of vegetation appears to take place too rapidly to maintain low rodent population densities over several years. The lack of studies prevented assessment of time lags in the qualitative responses of vegetation to rodent herbivory. We conclude that the literature is currently insufficient to discard with confidence any of the four potential hypotheses for plant-rodent cycles discussed herein. While new methods allow analyses of plant quality across more herbivore-relevant spatial scales than previously possible, we argue that the best way forward to rejecting any of the rodent-plant hypotheses is testing specific predictions of dietary variation. Indeed, all identified hypotheses make explicit assumptions on how rodent diet taxonomic composition and quality will change across the cycle. Passing this bottleneck could help pinpoint where, when, and how plant-herbivore interactions have - or do not have - plausible effects on rodent population dynamics.

Increased availability of preferred food and decreased foraging costs from degraded grasslands lead to rodent pests in the Qinghai-Tibet Plateau

The increased population density of rodent species during ongoing grassland degradation further deteriorates its conditions. Understanding the effects of grassland degradation on rodent feeding habits is of great value for optimizing grassland management strategies. In this study, lightly degraded (LD), moderately degraded (MD), severely degraded (SD), and reseeded grassland (RG) were selected and their plant resources and soil physical properties were investigated. In addition, the study used ITS2 barcode combined with the Illumina MiSeq sequencing method to analyze the food composition and proportion of plateau zokors in different grassland conditions. The results showed that, with grassland degradation, plant biomass decreased, but the relative proportion of forbs increased (LD: 32.05 ± 3.89%; MD: 28.97 ± 2.78%; SD: 49.16 ± 4.67% and RG: 10.93 ± 1.53%). Forbs were the main food of the plateau zokor, accounting for more than 90% of their diet, and the animal had a clear preference for Potentilla species; the soil compaction of feeding habits showed a decreasing trend in the 10–25 cm soil layer, suggesting a decreased foraging cost. Nutritional analysis showed that the stomach content of crude protein in zokors feeding on MD grassland was significantly higher than that of animals feeding on the other grassland types. Structural equation modeling showed that soil physical properties and the relative biomass of forbs had significant (P < 0.05) and extremely significant (P < 0.001) impacts on the population density of plateau zokors, with direct impact contribution rates of 0.20 and 0.63. As the severity of grassland degradation increased, although the aboveground and underground biomass of the plants decreased, the proportion of food preferred by the plateau zokor increased, and the corresponding changes in the feeding environment resulted in decreased foraging energy expenditure, thereby increasing the suitability of the degraded grassland for the plateau zokor. Compared with degraded grassland, the food diversity and evenness of zokors increased, the food niche width enlarged, and the proportion of weeds decreased in RG, which increased the difficulty of obtaining food. Reseeding in grassland management is therefore an effective way to control plateau zokors.

Multifaceted DNA Metabarcoding of Guano to Uncover Multiple Classes of Ecological Data in Two Different Bat Communities

DNA contained in animal scat provides a wealth of information about the animal, and DNA metabarcoding of scat collections can provide key information about animal populations and communities. Next‐generation DNA sequencing technologies and DNA metabarcoding provide an efficient means for obtaining information available in scat samples. We used multifaceted DNA metabarcoding (MDM) of noninvasively collected bat guano pellets from a Myotis lucifugus colony on Fort Drum Military Installation, New York, USA, and from two mixed‐species bat roosts on Fort Huachuca Military Installation, Arizona, USA, to identify attributes such as bat species composition, sex ratios, diet, and the presence of pathogens and parasites. We successfully identified bat species for nearly 98% of samples from Fort Drum and 90% of samples from Fort Huachuca, and identified the sex for 84% and 67% of samples from these same locations, respectively. Species and sex identification matched expectations based on prior censuses of bat populations utilizing those roosts, though samples from some species were more or less common than anticipated within Fort Huachuca roosts. Nearly 62% of guano samples from Fort Drum contained DNA from Pseudogymnoascus destructans, where bats with wing damage from White‐nose Syndrome were commonly observed. Putative dietary items were detected in a majority of samples from insectivorous bats on Fort Drum (81%) and Fort Huachuca (63%). A minority of guano samples identified as the nectarivorous Leptonycteris yerbabuenae (28%) provided DNA sequences from putative forage plant species. Finally, DNA sequences from both putative ecto‐ and endoparasite taxa were detected in 35% and 56% of samples from Fort Drum and Fort Huachuca, respectively. This study demonstrates that the combination of noninvasive sampling, DNA metabarcoding, and sample and locus multiplexing provide a wide array of data that are otherwise difficult to obtain.

DNA metabarcoding uncovers the diet of subterranean rodents in China

OBJECTIVE

A type of rodent called a zokor causes great harm to agriculture and forestry production due to its large and sophisticated diet. As this rodent lives subterrane for most of its life, researchers know little about its dietary habits. Further understanding of its diet is important for developing green and sustainable control strategies for the zokor.

METHODS

Chloroplast trnL gene and internal transcription spacer 1 primers were selected for high-throughput sequencing of stomach contents of captured zokor by DNA metabarcoding.

RESULTS

A total of 25 zokors were selected, the food list of 32 families, 80 genera, and 154 species was obtained. At the family level, it was found that zokors mainly fed on Asteraceae, Poaceae, Rosaceae, Pinaceae, Brassicaceae, and Apiaceae. At the genus level, zokors mainly fed on Echinops, Littledalea, Artemisia, Picea, Cirsium, and Elymus. The diet alpha diversity of Eospalax cansus was slightly higher than that of Eospalax cansus (P>0.05). The zokor's diet is highly phconsistent with the resources of its habitat. Most food choices tend to be the same between the two zokors. They fed primarily on Calamagrostis, Cirsium, Echinops, Medicago, Sanguisorba, and Taraxacum. Zokors mainly fed on the roots of perennial herbs, which are important source of energy.

CONCLUSION

High-throughput sequencing-based DNA metabarcoding technology has effectively revealed the diet of zokors and indicated that zokors are food generalists.

Redefining the Distributional Boundaries and Phylogenetic Relationships for Ctenomids From Central Argentina

With about 68 recognized living species, subterranean rodents of the genus Ctenomys are found in a multiplicity of habitats, from the dunes of the Atlantic coast to the Andes Mountains, including environments ranging from humid steppes of Pampas to the dry deserts of Chaco region. However, this genus needs an exhaustive reevaluation of its systematic and phylogenetic relationships regarding the different groups that compose it. This knowledge is essential to propose biodiversity conservation strategies both at species level and at higher hierarchical levels. In order to clarify the taxonomy and the recent evolutionary history from populations of Ctenomys in the Pampas region, Argentina, phylogenetic relationships among them were evaluated using mitochondrial DNA sequences: gene encoding cytochrome b protein (1,140 bp) and the non-coding D-loop region (434 bp). To infer the divergence times inside the Ctenomys clade, a Bayesian calibrate tree using fossil remains data from different families within Caviomorpha was performed at first. Secondly, that calibration data was used as priors in a new Bayesian phylogenetic inference within the genus Ctenomys. This phylogenetic tree emphasized on species currently distributed on the Pampas region, more precisely considering both the talarum and mendocinus groups. Bayesian inferences (BI) were integrated with the results of a Maximum Likelihood approach (ML). Based on these results, the distributional limits of the mendocinus and talarum groups appear to be related to the physiognomy of the Pampas region soils. On the other hand, the validity of C. pundti complex as a differentiated species of C. talarum is debated. According to previous evidence from morphological and chromosomal studies, these results show a very low divergence between those species that originally were classified within the talarum group. Mitochondrial DNA sequences from populations associated with these putative species have not recovered as reciprocal monophyletic groups in the phylogenetic analyses. In conclusion, C. talarum and C. pundti complex might be considered as the same biological species, or lineages going through a recent or incipient differentiation process. The results obtained in this study have important implications for conservation policies and practices, since both species are currently categorized as Vulnerable and Endangered, respectively.

eDNA metabarcoding for biodiversity assessment, generalist predators as sampling assistants

With an accelerating negative impact of anthropogenic actions on natural ecosystems, non-invasive biodiversity assessments are becoming increasingly crucial. As a consequence, the interest in the application of environmental DNA (eDNA) survey techniques has increased. The use of eDNA extracted from faeces from generalist predators, have recently been described as "biodiversity capsules" and suggested as a complementary tool for improving current biodiversity assessments. In this study, using faecal samples from two generalist omnivore species, the Eurasian badger and the red fox, we evaluated the applicability of eDNA metabarcoding in determining dietary composition, compared to macroscopic diet identification techniques. Subsequently, we used the dietary information obtained to assess its contribution to biodiversity assessments. Compared to classic macroscopic techniques, we found that eDNA metabarcoding detected more taxa, at higher taxonomic resolution, and proved to be an important technique to verify the species identification of the predator from field collected faeces. Furthermore, we showed how dietary analyses complemented field observations in describing biodiversity by identifying consumed flora and fauna that went unnoticed during field observations. While diet analysis approaches could not substitute field observations entirely, we suggest that their integration with other methods might overcome intrinsic limitations of single techniques in future biodiversity surveys.