Reconstructing a herbivore's diet using a novel rbcL DNA mini-barcode for plants

Dietary DNA metabarcoding reveals a trophic niche partitioning among sympatric Iberian sandgrouses and bustards

The study of trophic niche partitioning is of great importance for understanding community structure and species coexistence, particularly if these are threatened. Here DNA metabarcoding was used to assess the diet of four threatened steppe bird species (two bustards and two sandgrouses), with the aim of better understanding their dietary requirements, trophic interactions, and potential threats. The results showed seasonal and interspecific differences in their plant diet, with greater importance of cultivated plants during autumn and winter (around 50 % of their diet) than spring. Plants of the genus Convolvulus and of the family Brassicaceae were frequently consumed by all species. In spring, poppies (Papaver spp.) were a considerable part of their diet, and could be used as a source of carotenoids or for their anti-parasitic properties. Furthermore, results evidenced a trophic niche partitioning among species, with a marked segregation between bustard species and, to a lesser extent, between sandgrouse species. Diet similarity was generally higher between species from different orders that occur in mixed-species flocks (bustard - sandgrouse) than between species of the same order. This partitioning was probably related to a stratification in habitat use rather than to specialisation and might prevent competition to some extent. However, the homogenization of trophic resources resulting from agricultural intensification could pose an important threat, particularly during autumn, when weeds are scarcer and the most abundant trophic resource are sown seeds, which are often treated with pesticides.

Insect root feeders incur negative density-dependent damage across plant species in an alpine meadow

Although herbivores are well known to incur positive density-dependent damage and mortality, thereby likely shaping plant community assembly, the response of belowground root feeders to changes in plant density has seldom been addressed. Locally rare plant species (with lower plant biomass per area) are often smaller with shallower roots than common species (with higher plant biomass per area) in competition-intensive grasslands. Likewise, root feeders are often distributed in the upper soil layers. We hypothesized, therefore, that root feeders would incur negative density (biomass)-dependent damage across plant species. To test this hypothesis, we investigated the diversity and abundance of plant and root feeder species in an alpine meadow and determined the diet of the root feeders using metabarcoding. Across all species, root feeder load decreased with increasing aboveground plant biomass, root biomass, and total plant biomass per area, indicating a negative density dependence of damage across plant species. Aboveground plant biomass per area increased with increasing individual plant biomass and root depth per area across species, suggesting that rare plant species were smaller in size and had shallower root systems compared to common plant species. Both root biomass per area and root feeder biomass per area decreased with soil depth, but the root feeder biomass decreased disproportionately faster compared to root biomass with increasing root depth. Root feeder load decreased with increasing root depth but was not correlated with the feeding preference of root feeder species. Moreover, the prediction derived from a random process incorporating vertical distributions of root biomass and root feeder biomass significantly accounted for interspecific variation in root feeder load. In conclusion, the data indicate that root feeders incur negative density-dependent damage across plant species. On this basis, we suggest that manipulative experiments should be conducted to determine the effect of the negative density-dependent damage on plant community structure and that different types of plant-animal interactions should be concurrently examined to fully understand the effect of plant density on overall herbivore damage across plant species.

Metabarcoding analysis provides insight into the link between prey and plant intake in a large alpine cat carnivore, the snow leopard

Species of the family Felidae are thought to be obligate carnivores. However, detection of plants in their faeces raises questions about the role of plants in their diet. This is particularly true for the snow leopard (Panthera uncia). Our study aimed to comprehensively identify the prey and plants consumed by snow leopards. We applied DNA metabarcoding methods on 90 faecal samples of snow leopards collected in Kyrgyzstan, employing one vertebrate and four plant markers. We found that argali (Ovis ammon) was detected only from male snow leopards. Myricaraia sp. was the most consumed among 77 plant operational taxonomic units found in snow leopard samples. It frequently appeared in samples lacking any prey animal DNA, indicating that snow leopards might have consumed this plant especially when their digestive tracts were empty. We also observed differences in the patterns of plant consumption between male and female snow leopards. Our comprehensive overview of prey and plants detected in the faeces of snow leopards and other sympatric mammals will help in formulating hypotheses and guiding future research to understand the adaptive significance of plant-eating behaviour in felids. This knowledge supports the enhancement of their captive environments and the conservation planning of their natural habitats.

Finding the perfect pairs: A matchmaking of plant markers and primers for multi-marker eDNA metabarcoding

As the scope of plant eDNA metabarcoding diversifies, so do the primers, markers and methods. A wealth of primers exists today, but their comparative evaluation is lacking behind. Similarly, multi-marker approaches are recommended but debates persist regarding barcode complementarity and optimal combinations. After a literature compilation of used primers, we compared in silico 102 primer pairs based on amplicon size, coverage and specificity, followed by an experimental evaluation of 15 primer pairs on a mock community sample covering 268 plant species and genera, and about 100 families. The analysis was done for the four most common plant metabarcoding markers, rbcL, trnL, ITS1 and ITS2 and their complementarity was assessed based on retrieved species. By focusing on existing primers, we identify common designs, promote alternatives and enhance prior-supported primers for immediate applications. The ITS2 was the best-performing marker for flowering vascular plants and was congruent to ITS1. However, the combined taxonomic breadth of ITS2 and rbcL surpassed any other combination, highlighting their high complementarity across Streptophyta. Overall, our study underscores the significance of comprehensive primer and barcode evaluations tailored to metabarcoding applications.

Sea Snacks from DNA Tracks: Using DNA Metabarcoding to Characterize The Diet of Green Turtles (Chelonia Mydas)

The green turtle (Chelonia mydas) is a circumglobal species with a wide dietary breadth that varies among regions and life history stages. Comprehensive understanding of foraging ecology over space and time is critical to inform conservation and management of this species and its habitats. Here, we used DNA metabarcoding to test candidate primer sets with 39 gut content homogenates from stranded green turtles (FL, USA) to identify primer sets that maximize detection of food items and specificity of taxonomic classifications. We tested six existing universal primer sets to detect plants, animals, and eukaryotes more broadly (CO1, 18SV1-V3, 18SV4, rbcL, UPA, ITS). The CO1 and 18SV4 primer sets produced the greatest number of dietary amplicon sequence variants (ASVs) and unique taxonomic classifications, and they were the only primer sets to amplify taxa from all three kingdoms relevant to green turtle diet (Animalia, Chromista, and Plantae). Even though the majority of CO1-derived reads were of host origin (>90%), this primer set still produced the largest number of dietary ASVs classified to species among the six primer sets. However, because the CO1 primer set failed to detect both vascular plants and green algae, we do not recommend the use of this primer set on its own to characterize green turtle diet. Instead, our findings support previous research highlighting the utility of using multiple primer sets, specifically targeting CO1 and the V4 region of the 18S gene, as doing so will provide the most comprehensive understanding of green turtle diet. More generally, our results highlight the importance of primer and loci selection and the need to validate primer sets against the study system of interest. The addition of DNA metabarcoding with optimized primer sets to the sea turtle researcher's toolbox will both increase our understanding of foraging ecology and better inform science-based conservation and ecosystem management.

Advances and Limitations of Next Generation Sequencing in Animal Diet Analysis

Diet analysis is a critical content of animal ecology and the diet analysis methods have been constantly improving and updating. Contrary to traditional methods of high labor intensity and low resolution, the next generation sequencing (NGS) approach has been suggested as a promising tool for dietary studies, which greatly improves the efficiency and broadens the application range. Here we present a framework of adopting NGS and DNA metabarcoding into diet analysis, and discuss the application in aspects of prey taxa composition and structure, intra-specific and inter-specific trophic links, and the effects of animal feeding on environmental changes. Yet, the generation of NGS-based diet data and subsequent analyses and interpretations are still challenging with several factors, making it possible still not as widely used as might be expected. We suggest that NGS-based diet methods must be furthered, analytical pipelines should be developed. More application perspectives, including nutrient geometry, metagenomics and nutrigenomics, need to be incorporated to encourage more ecologists to infer novel insights on they work.

Visualization of the seasonal shift of a variety of airborne pollens in western Tokyo

Airborne pollens cause pollinosis and have the potential to affect microphysics in clouds; however, the number of monitored species has been very limited due to technical difficulties for the morphotype identification. In this study, we applied an eDNA approach to the airborne pollen communities in the suburbs of the Tokyo metropolitan area in Japan, within a mixed urban, rural, and mountain landscape, revealing pollen seasonality of various taxa (a total of 78 families across the period) in the spring season (February to May). Those taxa distinctly shifted in the season, especially in the beginning of February and the middle of April. Air temperature shift was an obvious key factor to affect the airborne pollen community, while the influence of other meteorological factors, such as wind speed, humidity, and precipitation, was not clear. Taxonomic classification of major Amplicon Sequence Variants (ASVs) indicates multiple pollen sources, including natural forest, planted forest, roadside, park lands, and horticultural activities. Most major ASV belongs to Japanese cedar (Cryptomeria japonica), which is the most notable allergen that causes pollinosis in Japan, peaking in mid-February to March. Backward trajectory analysis of air masses suggests that the Japanese cedar and other Cupressaceae plantation forests in the western mountains were a significant source of airborne pollen communities detected at our sampling site. Other major plant pollen sources, including Japanese zelkova (Zelkova serrata) and ginkgo (Ginkgo biloba), emanated from the nearby parks or roadside regions. This study's approach enables us to visualize the phenology of multiple pollen, including timing and duration. Long-term monitoring of this type would provide additional insight into understanding the role of climate change on pollen transmission and links to flowering events.

Using Fecal DNA Metabarcoding to Investigate Foraging Reveals the Effects of Specific Herbage on the Improved n-3 Fatty Acid (PUFA) Composition in the Longissimus Dorsi Muscle of Grazing Tan Sheep

Understanding the natural diet of grazing sheep can help fulfill their nutritional requirements and positively affect the quality of their meat. Emerging fecal DNA (fDNA) metabarcoding technology can provide more accurate estimates for the dietary composition of free-ranging animals. This study has shown that pasture feeding can promote deposition of n-3 polyunsaturated fatty acids (PUFAs) in Tan lambs' muscle and decrease the ratio of n-6/n-3 fatty acids (FAs), and thus, we investigated the dietary composition of grazing lambs using fDNA metabarcoding to assess the prevalence of medicinal herbage plants in their diet. Herein, based on the full-time natural pasture grazing and 4-h natural pasture grazing with indoor feeding patterns, the herbage taxa (Bassia scoparia, Euphorbia humifusa, Arnebia euchroma, and Salsola sp.) most correlated to n-3 PUFAs were highlighted to elucidate how diversification in dietary components was associated with the muscle FA profile of lambs. Our findings provide experimental evidence for future feeding research.

HPLC-UV, Metabarcoding and Genome Skims of Botanical Dietary Supplements: A Case Study in Echinacea

The use of DNA-based methods to authenticate botanical dietary supplements has been vigorously debated for a variety of reasons. More comparisons of DNA-based and chemical methods are needed, and concordant evaluation of orthogonal approaches on the same products will provide data to better understand the strengths and weaknesses of both approaches. The overall application of DNA-based methods is already firmly integrated into a wide array of continually modernizing stand alone and complementary authentication protocols. Recently, the use of full-length chloroplast genome sequences provided enhanced discriminatory capacity for closely related species of Echinacea compared to traditional DNA barcoding approaches (matK and rbcL). Here, two next-generation sequencing approaches were used: (1) genome skimming and (2) PCR amplicon (metabarcoding). The two genetic approaches were then combined with HPLC-UV to evaluate 20 commercially available dietary supplements of Echinacea representing "finished" products. The trade-offs involved in different DNA approaches were discussed, with a focus on how DNA methods support existing, accepted chemical methods. In most of the products (19/20), HPLC-UV suggested the presence of Echinacea spp. While metabarcoding was not useful with this genus and instead only resolved 7 products to the family level, genome skimming was able to resolve to species (9) or genus (1) with the 10/20 products where it was successful. Additional ingredients that HPLC-UV was unable to identify were also found in four products along with the relative sequence proportion of the constituents. Additionally, genome skimming was able to identify one product that was a different Echinacea species entirely.

Isotope analysis combined with DNA barcoding provide new insights into the dietary niche of khulan in the Mongolian Gobi

With increasing livestock numbers, competition and avoidance are increasingly shaping resource availability for wild ungulates. Shifts in the dietary niche of wild ungulates are likely and can be expected to negatively affect their fitness. The Mongolian Gobi constitutes the largest remaining refuge for several threatened ungulates, but unprecedentedly high livestock numbers are sparking growing concerns over rangeland health and impacts on threatened ungulates like the Asiatic wild ass (khulan). Previous stable isotope analysis of khulan tail hair from the Dzungarian Gobi suggested that they graze in summer but switch to a poorer mixed C3 grass / C4 shrub diet in winter, most likely in reaction to local herders and their livestock. Here we attempt to validate these findings with a different methodology, DNA metabarcoding. Further, we extend the scope of the original study to the South Gobi Region, where we expect higher proportions of low-quality browse in the khulan winter diet due to a higher human and livestock presence. Barcoding confirmed the assumptions behind the seasonal diet change observed in the Dzungarian Gobi isotope data, and new isotope analysis revealed a strong seasonal pattern and higher C4 plant intake in the South Gobi Region, in line with our expectations. However, DNA barcoding revealed C4 domination of winter diet was due to C4 grasses (rather than shrubs) for the South Gobi Region. Slight climatic differences result in regional shifts in the occurrence of C3 and C4 grasses and shrubs, which do not allow for an isotopic separation along the grazer-browser continuum over the entire Gobi. Our findings do not allow us to confirm human impacts upon dietary preferences in khulan as we lack seasonal samples from the South Gobi Region. However, these data provide novel insight into khulan diet, raise new questions about plant availability versus preference, and provide a cautionary tale about indirect analysis methods if used in isolation or extrapolated to the landscape level. Good concordance between relative read abundance of C4 genera from barcoding and proportion of C4 plants from isotope analysis adds to a growing body of evidence that barcoding is a promising quantitative tool to understand resource partitioning in ungulates.

Molecular Evolution of rbcL in Orthotrichales (Bryophyta): Site Variation, Adaptive Evolution, and Coevolutionary Patterns of Amino Acid Replacements

Molecular evolution of the large subunit of the RuBisCO enzyme is understudied in early diverging land plants. These groups show morphological and eco-physiological adaptations to the uneven and intermittent distribution of water in the terrestrial environment. This might have prompted a continuous fine-tuning of RuBisCO under a selective pressure modifying the species-specific optima for photosynthesis in contrasting microdistributions and environmental niches. To gain a better insight into the molecular evolution of RuBisCO large subunits, the aim of this study was to assess the pattern of evolutionary change in the amino acid residues in a monophyletic group of Bryophyta (Orthotrichaceae). Tests for positive, neutral, or purifying selection at the amino acid level were assessed by comparing rates (ω) of non-synonymous (d_N) and synonymous (d_S) nucleotide substitutions along a Maximum Likelihood phylogenetic tree. Molecular adaptation tests using likelihood ratio tests, reconstruction of ancestral amino acid sites, and intra-protein coevolution analyses were performed. Variable amino acid sites (39) were unevenly distributed across the LSU. The residues are located on rbcL sites that are highly variable in higher plants and close to key regions implying dimer-dimer (L₂L₂), RuBisCO-activase interactions, and conformational functions during catalysis. Ten rbcL sites (32, 33, 91, 230, 247, 251, 255, 424, 449 and 475) have been identified by the Bayesian Empirical Bayes inference to be under positive selection and under adaptive evolution under the M8 model. The pattern of amino acid variation suggests that it is not lineage specific, but rather representative of a case of convergent evolution, suggesting recurrent changes that potentially favor the same amino acid substitutions that are likely optimized the RuBisCO activity.

A multi-kingdom metabarcoding study on cattle grazing Alpine pastures discloses intra-seasonal shifts in plant selection and faecal microbiota

Diet selection by grazing livestock may affect animal performance as well as the biodiversity of grazed areas. Recent DNA barcoding techniques allow to assess dietary plant composition in faecal samples, which may be additionally integrated by the description of gut microbiota. In this high throughput metabarcoding study, we investigated the diversity of plant, fungal and bacterial taxa in faecal samples of lactating cows of two breeds grazing an Alpine semi-natural grassland during summer. The estimated plant composition of the diet comprised 67 genera and 39 species, which varied remarkably during summer, suggesting a decline of the diet forage value with the advancing of the vegetative season. The fungal community included Neocallimastigomycota gut symbionts, but also Ascomycota and Basidiomycota plant parasite and coprophilous taxa, likely ingested during grazing. The proportion of ingested fungi was remarkably higher than in other studies, and varied during summer, although less than that observed for plants. Some variation related to breed was also detected. The gut bacterial taxa remained stable through the summer but displayed a breed-specific composition. The study provided insights in the reciprocal organisms' interactions affecting, and being affected by, the foraging behaviour: plants showed a high temporal variation, fungi a smaller one, while bacteria had practically none; conversely, the same kingdoms showed the opposite gradient of variation as respect to the animal host breed, as bacteria revealed to be the group mostly characterized by host-specificity.

Using pollen DNA metabarcoding to profile nectar sources of urban beekeeping in Kōtō-ku, Tokyo

Objective

Apis mellifera is a species of honeybee that has been introduced around the world as an industrial beekeeping species. Recently, urban beekeeping has attracted attention as a means of ecosystem protection and urban greening. This study aimed to investigate nectar sources of urban beekeeping in Kōtō-ku, Tokyo using pollen DNA metabarcoding.

Results

We extracted DNA from pollen collected by the honeybees of a local urban beekeeping operation. DNA metabarcoding analysis was carried out by sequencing a part of the rbcL region of the chloroplast genome. A total of 31 samples collected between mid-March, 2018 and mid-October, 2018 yielded 54 operational taxonomic units (OTUs) comprising 14 families, 32 genera, and 8 species. Whereas 5 OTUs were profiled throughout all seasons, 38 OTUs were season-specific (spring, summer, or autumn). Therefore, we were able to infer seasonal nectar sources for the beekeeping operation at the family or genus level, as well as at the species level to a lesser extent. Our pollen-sampling strategy was effective for profiling season-specific nectar sources, with the exception of a few anomalies that can be accounted for by out-of-season flowering associated with artificial gardening and/or pollen accumulation over multiple seasons.

Employing DNA metabarcoding to determine the geographical origin of honey

Unfavourable climatic conditions force Iranian beekeepers to translocate over large distances in the course of the year. However, irrespective of the main place of production, the honey is always labeled with the name of the beekeepers' hometown, which leads consequently to mislabeled products. The present study investigates the capability of DNA metabarcoding to locate the geographical origin of honey. The molecular markers (ITS2 and rbcL) allowed identification of 926 plant species in studied samples. A comprehensive review of floristic reference books specified 34 key species that could be used to successfully determine the geographical origin in 91.4% of samples. These key species were usually present in honey with tiny amounts and thus, conventional palynology might not be able to detect them. The present investigation indicates that although ITS2 is able to detect more species than rbcL, utilizing a combination of both markers provides more robust evidence of geographical origin.

First DNA sequence reference library for mammals and plants of the Eastern Mediterranean Region

The Mediterranean region is identified as one of the world's 36 biodiversity hotspots, with the Earth's most biologically rich yet threatened areas. Lebanon is a hub for Eastern Mediterranean Region (EMR) biodiversity with 9116 characterized plant and animal species (4486 fauna and 4630 flora). Using DNA barcoding as a tool has become crucial in the accurate identification of species in multiple contexts. It can also complement species morphological descriptions, which will add to our understanding of the biodiversity and richness of ecosystems and benefit conservation projects for endangered and endemic species. In this study, we create the first reference library of standard DNA markers for mammals and plants in the EMR, with a focus on endemic and endangered species. Plant leaves were collected from different nature reserves in Mount Lebanon, and mammal samples were obtained from taxidermized museum specimens or road kills. We generated the 12S rRNA sequences of 18 mammal species from 6 orders and 13 different families. We also obtained the trnL and rbcL barcode sequences of 52 plant species from 24 different families. Twenty-five plant species and two mammal species included in this study were sequenced for the first time using these markers.

Red oak seedlings as indicators of deer browse pressure: Gauging the outcome of different white-tailed deer management approaches

After decades of high deer populations, North American forests have lost much of their previous biodiversity. Any landscape-level recovery requires substantial reductions in deer herds, but modern societies and wildlife management agencies appear unable to devise appropriate solutions to this chronic ecological and human health crisis. We evaluated the effectiveness of fertility control and hunting in reducing deer impacts at Cornell University. We estimated spring deer populations and planted Quercus rubra seedlings to assess deer browse pressure, rodent attack, and other factors compromising seedling performance. Oak seedlings protected in cages grew well, but deer annually browsed ≥60% of unprotected seedlings. Despite female sterilization rates of >90%, the deer population remained stable. Neither sterilization nor recreational hunting reduced deer browse rates and neither appears able to achieve reductions in deer populations or their impacts. We eliminated deer sterilization and recreational hunting in a core management area in favor of allowing volunteer archers to shoot deer over bait, including at night. This resulted in a substantial reduction in the deer population and a linear decline in browse rates as a function of spring deer abundance. Public trust stewardship of North American landscapes will require a fundamental overhaul in deer management to provide for a brighter future, and oak seedlings may be a promising metric to assess success. These changes will require intense public debate and may require new approaches such as regulated commercial hunting, natural dispersal, or intentional release of important deer predators (e.g., wolves and mountain lions). Such drastic changes in deer management will be highly controversial, and at present, likely difficult to implement in North America. However, the future of our forest ecosystems and their associated biodiversity will depend on evidence to guide change in landscape management and stewardship.

Host plant use of a polyphagous mirid, Apolygus lucorum: Molecular evidence from migratory individuals

While the host plant use of insect herbivores is important for understanding their interactions and coevolution, field evidence of these preferences is limited for generalist species. Molecular diet analysis provides an effective option for gaining such information, but data from field-sampled individuals are often greatly affected by the local composition of their host plants. The polyphagous mirid bug Apolygus lucorum (Meyer-Dür) seasonally migrates across the Bohai Sea, and molecular analysis of migrant bugs collected on crop-free islands can be used to estimate the host plant use of A. lucorum across the large area (northern China) from where these individuals come. In this study, the host plant use of A. lucorum adults was determined by identifying plant DNA using a three-locus DNA barcode (rbcL, trnH-psbA, and ITS) in the gut of migrant individuals collected on Beihuang Island. We successfully identified the host plant families of A. lucorum adults, and the results indicated that captured bugs fed on at least 17 plant families. In addition, gut analyses revealed that 35.9% of A. lucorum individuals fed on multiple host plants but that most individuals (64.1%) fed on only one plant species. Cotton, Gossypium hirsutum L., DNA was found in 35.8% of the A. lucorum bugs examined, which was much higher than the percentage of bugs in which other host plants were found. Our work provides a new understanding of multiple host plant use by A. lucorum under natural conditions, and these findings are available for developing effective management strategies against this polyphagous pest species.

Seeing is believing? Comparing plant-herbivore networks constructed by field co-occurrence and DNA barcoding methods for gaining insights into network structures

Plant-herbivore interaction networks provide information about community organization. Two methods are currently used to document pairwise interactions among plants and insect herbivores. One is the traditional method that collects plant-herbivore interaction data by field observation of insect occurrence on host plants. The other is the increasing application of newly developed molecular techniques based on DNA barcodes to the analysis of gut contents. The second method is more appealing because it documents realized interactions. To construct complete interaction networks, each technique of network construction is urgent to be assessed. We addressed this question by comparing the effectiveness and reliability of the two methods in constructing plant-Lepidoptera larval network in a 50 ha subtropical forest in China. Our results showed that the accuracy of diet identification by observation method increased with the number of observed insect occurrences on food plants. In contrast, the molecular method using three plant DNA markers were able to identify food residues for 35.6% larvae and correctly resolved 77.3% plant (diet) species. Network analysis showed molecular networks had threefold more unique host plant species but fewer links than the traditional networks had. The molecular method detected plants that were not sampled by the traditional method, for example, bamboos, bryophytes and lianas in the diets of insect herbivores. The two networks also possessed significantly different structural properties. Our study indicates the traditional observation of co-occurrence is inadequate, while molecular method can provide higher species resolution of ecological interactions.

trnL outperforms rbcL as a DNA metabarcoding marker when compared with the observed plant component of the diet of wild white-faced capuchins (Cebus capucinus, Primates)

DNA metabarcoding is a powerful tool for assessing the diets of wild animals, but there is no clear consensus on which proposed plant barcoding marker is most suitable for dietary analysis. This study compares two DNA plant barcoding markers that are commonly used for dietary analyses from degraded DNA, rbcL and trnL, to detailed dietary observations of wild white-faced capuchins (Cebus capucinus). Observational dietary data and fecal samples (n = 170) were collected for one year from a group of individually recognizable monkeys at La Suerte Biological Field Station, Costa Rica. DNA was extracted and portions of the rbcL and trnL chloroplast were amplified and sequenced on the Illumina MiSeq platform. Sequences were analyzed using obitools. Of the two barcoding markers tested, trnL yielded greater numbers of sequences with equal sequencing effort, higher resolution taxonomic identifications (albeit with a larger reference database), and identified a greater number of families also found in the observed diet. There was no relationship between observed capuchin feeding behavior and dietary composition based on either sequence occurrence or relative abundance of sequences using rbcL as a marker. However, dietary composition based on the relative abundance of trnL sequences was significantly positively associated with the observed percentage of feeding and foraging time capuchins' spent on each plant species. Additionally, in 35% of cases, the relative abundance of trnL sequences assigned to particular plant families in fecal samples was highly positively correlated with time spent consuming plants from those same families. Our results indicate that trnL is a more robust DNA metabarcoding marker for plant dietary analysis and may potentially be used to quantitatively assess differences in diet within or between species.

Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

Advances in DNA sequencing technology have revolutionized the field of molecular analysis of trophic interactions, and it is now possible to recover counts of food DNA sequences from a wide range of dietary samples. But what do these counts mean? To obtain an accurate estimate of a consumer's diet should we work strictly with data sets summarizing frequency of occurrence of different food taxa, or is it possible to use relative number of sequences? Both approaches are applied to obtain semi-quantitative diet summaries, but occurrence data are often promoted as a more conservative and reliable option due to taxa-specific biases in recovery of sequences. We explore representative dietary metabarcoding data sets and point out that diet summaries based on occurrence data often overestimate the importance of food consumed in small quantities (potentially including low-level contaminants) and are sensitive to the count threshold used to define an occurrence. Our simulations indicate that using relative read abundance (RRA) information often provides a more accurate view of population-level diet even with moderate recovery biases incorporated; however, RRA summaries are sensitive to recovery biases impacting common diet taxa. Both approaches are more accurate when the mean number of food taxa in samples is small. The ideas presented here highlight the need to consider all sources of bias and to justify the methods used to interpret count data in dietary metabarcoding studies. We encourage researchers to continue addressing methodological challenges and acknowledge unanswered questions to help spur future investigations in this rapidly developing area of research.

Using herbarium-derived DNAs to assemble a large-scale DNA barcode library for the vascular plants of Canada

PREMISE OF THE STUDY

Constructing complete, accurate plant DNA barcode reference libraries can be logistically challenging for large-scale floras. Here we demonstrate the promise and challenges of using herbarium collections for building a DNA barcode reference library for the vascular plant flora of Canada.

METHODS

Our study examined 20,816 specimens representing 5076 of 5190 vascular plant species in Canada (98%). For 98% of the specimens, at least one of the DNA barcode regions was recovered from the plastid loci rbcL and matK and from the nuclear ITS2 region. We used beta regression to quantify the effects of age, type of preservation, and taxonomic affiliation (family) on DNA sequence recovery.

RESULTS

Specimen age and method of preservation had significant effects on sequence recovery for all markers, but influenced some families more (e.g., Boraginaceae) than others (e.g., Asteraceae).

DISCUSSION

Our DNA barcode library represents an unparalleled resource for metagenomic and ecological genetic research working on temperate and arctic biomes. An observed decline in sequence recovery with specimen age may be associated with poor primer matches, intragenomic variation (for ITS2), or inhibitory secondary compounds in some taxa.

Introduction to the Special Issue: Ungulates and invasive species: quantifying impacts and understanding interactions

White-tailed deer are emblematic ungulates that, due to anthropogenic modification of landscapes, currently occur at elevated densities. Elevated deer densities often co-occur with non-native plants, but it is not known if plant invasions are a consequence of deer impacts or occur independent of deer impacts on ecosystems, or whether these two stressors are synergistic. A colloquium on 'Interactions of white-tailed deer and invasive plants in forests of eastern North America' explored these topics at the 2016 annual meeting of the Botanical Society of America. Nine of those presentations are published in this special issue of AoB PLANTS.

White-tailed deer browse on an invasive shrub with extended leaf phenology meets assumptions of an apparent competition hypothesis

It has been hypothesized that invasive plant species with extended leaf phenology (ELP) elevate generalist herbivore populations, increasing herbivory on native plants (apparent competition). This hypothesis assumes that consumption of the invasive is associated with periods of ELP, the invasive is a major component of the herbivore's diet, and that it is more nutritious than native plants during periods of ELP. We tested these assumptions by estimating the proportion of the white-tailed deer diet comprised of Lonicera maackii, an invasive shrub with ELP, quantifying the seasonal pattern of deer browse on this invasive shrub, and comparing its nutritional quality to leafless woody stems. In the Miami University Natural Areas in southwest Ohio we quantified the frequency of leafy twigs of woody species 0.3-2.1 m high in three habitats (deciduous forest, Juniperus virginiana forest, and forest-field edge). Monthly we quantified deer browse on marked L. maackii twigs, and estimated the mass of leaf and stem tissue consumed with allometric relationships using diameter and length of unbrowsed twig portions. We estimated the percent of the annual deer diet comprised of L. maackii by dividing the sum of these estimates by the product of deer abundance (estimated by pellet-based distance sampling) and consumption estimates from the literature. Crude protein of L. maackii stems and leaves was determined by C:N analyser. In each habitat the frequency of L. maackii was greater than all other woody species combined. We estimated L. maackii comprised 14-47 % of the annual deer diet. Deer browsed L. maackii each month, but consumption was high in early spring and late summer. Crude protein of leafy twigs of L. maackii in early spring was 12.9 %, much higher than leafless twigs of native species on-site. These findings support the assumptions of the hypothesis that invasive plants with ELP impact native plants via deer-mediated apparent competition.