A diet rich in C3 plants reveals the sensitivity of an alpine mammal to climate change

An experimental design for obtaining DNA of a target species and its diet from a single non-invasive genetic protocol

Next-generation sequencing technology has enabled accurate insights into the diet of wildlife species. The protocols for faecal sample collection and DNA extraction for diet analysis have differed from those focusing on target species, even in most studies combining questions on both aspects. We designed an experiment to evaluate two protocols using 11 parameters and select a single one that will generate both target species (Asiatic wild ass, Equus hemionus, in Israel) and diet DNA, as an effective strategy to minimise time, effort, and cost without hampering efficiency. In Protocol A, we swabbed the outer surface of faecal boluses and extracted DNA using a Stool Kit, while for Protocol B, we homogenised faecal matter from inside the bolus followed by extraction using a Powersoil Kit. Protocol A performed significantly better for four parameters, which included, for the target species, microsatellite amplification success and the quantity of the GAPDH gene; and for its diet, the number of exact sequence variants (ESVs) obtained at genus level and plant genus richness. However, there was no significant difference in the amplification success of sex-linked and plant markers, total reads at genus level, number of genera obtained and plant genus composition. Although we chose Protocol A, both protocols yielded results for the target species and its diet, demonstrating that one single protocol can be used for both purposes, although a pilot study is recommended to optimise the protocol for specific systems. This strategy may also be useful for studies combining target species and their gut microbiome and parasitic load.

Introducing an rbcL and a trnL reference library to aid in the metabarcoding analysis of foraged plants from two semi-arid eastern South African savanna bioregions

Success of a metabarcoding study is determined by the extent of taxonomic coverage and the quality of records available in the DNA barcode reference database used. This study aimed to create an rbcL and a trnL (UAA) DNA barcode sequence reference database of plant species that are potential herbivore foraging targets and commonly found in semi-arid savannas of eastern South Africa. An area-specific species list of 765 species was compiled according to plant collection records available and areas comparable to an eastern semi-arid South African savanna. Thereafter, rbcL and trnL sequences of species from this list were mined from GenBank and BOLD sequence databases according to specific quality criteria to ensure accurate taxonomic coverage and resolution. These were supplemented with sequences of 24 species sequenced for this study. A phylogenetic approach, employing Neighbor-Joining, was used to verify the topology of the reference libraries to known angiosperm phylogeny. The taxonomic reliability of these reference libraries was evaluated by testing for the presence of a barcode gap, identifying a data-appropriate identification threshold, and determining the identification accuracy of reference sequences via primary distance-based criteria. The final rbcL reference dataset consisted of 1238 sequences representing 318 genera and 562 species. The final trnL dataset consisted of 921 sequences representing 270 genera and 461 species. Barcode gaps were found for 76% of the taxa in the rbcL barcode reference dataset and 68% of the taxa in the trnL barcode reference dataset. The identification success rate, calculated with the k-nn criterion was 85.86% for the rbcL dataset and 73.72% for the trnL dataset. The datasets for rbcL and trnL combined during this study are not presented as complete DNA reference libraries, but rather as two datasets that should be used in unison to identify plants present in the semi-arid eastern savannas of South Africa.

The pikas of China: a review of current research priorities and challenges for conservation

Of the approximately 30 extant species of pika (Ochotona; Ochotonidae; Lagomorpha), at least 23 occur in China. Of these, 8 are endemic, and 3 are classified as Endangered by the IUCN. Research into most Chinese species is scarce, and there is much to learn about basic aspects of their ecology. We reviewed the literature on the 23 Chinese Ochotona species, with the aim of highlighting knowledge gaps and biases in research allocation. Specifically, we identify (1) which pika species receive the most attention from researchers, (2) which topics are the most frequently studied, and (3) how well research satisfies conservation priorities. We covered a total of 879 articles, most of which were written in English or Chinese. Around 75% of all publications focused on the plateau pika Ochotona curzoniae. Seven species were represented by 10 or fewer publications each. Endangered and endemic species were particularly poorly represented. 204 papers treated pikas as a pest, while 13 studied conservation issues. Nine species were considered possible targets for pest control, including some poorly known endemics. We make some recommendations on how research into Chinese Ochotona could be improved, including: (1) recognizing that the current species-level taxonomy may be an ineffective way to prioritize conservation research in Ochotona, (2) directing more research toward threatened and endemic species, subspecies, and populations, (3) researching the ecosystem engineering effects of pikas, (4) collecting basic data on natural history of the many understudied species, and (5) researching threats, including climate change and pest control campaigns.

Diet preferences based on sequence read count: the role of species interaction in tissue bias correction

High-throughput sequencing and metabarcoding techniques provide a unique opportunity to study predator-prey relationships. However, in animal dietary preference studies, how to properly correct tissue bias within the sequence read count and the role of interactions between co-occurring species in metabarcoding mixtures remain largely unknown. In this study, we proposed two categories of tissue bias correction indices: sequence read count number per unit tissue (SCN) and its ratio form (SCN ratio). By constructing plant mock communities with different numbers of co-occurring species in metabarcoding mixtures and conducting feeding trails on captive sika deer (Cervus nippon), we demonstrated the features of the SCN and SCN ratio, evaluated their correction effects, and assessed the role of species interactions during tissue bias correction. Tissue differences between species are defined as the differential ability in generating sequence counts. Our study suggests that pure tissue differences among species without species interaction is not an optimal correction index for many biomes with limited tissue differences among species. Species interactions in mixtures may amplify tissue differences, which is beneficial for tissue bias correction. However, caution must be taken because varied species interaction among communities may increase the risk of worse correction. Correction effects based on the SCN and SCN ratio are comparable, while the SCN is less influenced by control species than the SCN ratio. According to our study, several suggestions were provided for future animal diet studies or other high-throughput sequencing studies containing tissue bias.

Environmental DNA analysis as an emerging non-destructive method for plant biodiversity monitoring: a review

Environmental DNA (eDNA) analysis has recently transformed and modernized biodiversity monitoring. The accurate detection, and to some extent quantification, of organisms (individuals/populations/communities) in environmental samples is galvanizing eDNA as a successful cost and time-efficient biomonitoring technique. Currently, eDNA's application to plants remains more limited in implementation and scope compared to animals and microorganisms. This review evaluates the development of eDNA-based methods for (vascular) plants, comparing its performance and power of detection with that of traditional methods, to critically evaluate and advise best-practices needed to innovate plant biomonitoring. Recent advancements, standardization and field applications of eDNA-based methods have provided enough scope to utilize it in conservation biology for numerous organisms. Despite our review demonstrating only 13% of all eDNA studies focus on plant taxa to date, eDNA has considerable environmental DNA has considerable potential for plants, where successful detection of invasive, endangered and rare species, and community-level interpretations have provided proof-of-concept. Monitoring methods using eDNA were found to be equal or more effective than traditional methods; however, species detection increased when both methods were coupled. Additionally, eDNA methods were found to be effective in studying species interactions, community dynamics and even effects of anthropogenic pressure. Currently, elimination of potential obstacles (e.g. lack of relevant DNA reference libraries for plants) and the development of user-friendly protocols would greatly contribute to comprehensive eDNA-based plant monitoring programs. This is particularly needed in the data-depauperate tropics and for some plant groups (e.g., Bryophytes and Pteridophytes). We further advocate to coupling traditional methods with eDNA approaches, as the former is often cheaper and methodologically more straightforward, while the latter offers non-destructive approaches with increased discrimination ability. Furthermore, to make a global platform for eDNA, governmental and academic-industrial collaborations are essential to make eDNA surveys a broadly adopted and implemented, rapid, cost-effective and non-invasive plant monitoring approach.

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.

Near Infrared Reflectance Spectroscopy Analysis to Predict Diet Composition of a Mountain Ungulate Species

Simple Summary

Ungulates are characterized by their ability to modify or maintain habitats through their impact on plant species composition and the structure of vegetation. Assessing the diet composition of ungulates is therefore important to understand their role in the ecosystem integrity and to develop monitoring and population management plans. The diet composition of free-ranging ungulates has most often been assessed by time-consuming and cost-intensive approaches such as the direct observation of animals, chemical analysis, molecular approaches or microhistological analysis of fecal samples. Near infrared reflectance spectroscopy analysis would be a quick, economic and non-destructive alternative to assess diet composition using fecal samples. In this work, we evaluated the use of this spectroscopy method to assess the diet composition of the Pyrenean chamois (Rupicapra pyrenaica pyrenaica), a medium-size subalpine ungulate with a broad dietary niche. Our results support the reliability of the fecal spectroscopy analysis to monitor diet composition of free-ranging ungulates.

Abstract

The diet composition of ungulates is important to understand not only their impact on vegetation, but also to understand the consequences of natural and human-driven environmental changes on the foraging behavior of these mammals. In this work, we evaluated the use of near infrared reflectance spectroscopy analysis (NIRS), a quick, economic and non-destructive method, to assess the diet composition of the Pyrenean chamois Rupicapra pyrenaica pyrenaica. Fecal samples (n = 192) were collected from two chamois populations in the French and Spanish Pyrenees. Diet composition was initially assessed by fecal cuticle microhistological analysis (CMA) and categorized into four functional groups, namely: woody, herbaceous, graminoid and Fabaceae plants. Regressions of modified partial least squares and several combinations of scattering correction and derivative treatments were tested. The results showed that models based on the second derivative processing obtained the higher determination coefficient for woody, herbaceous and graminoid plants (R²_CAL, coefficient of determination in calibration, ranged from 0.86 to 0.91). The Fabaceae group, however, was predicted with lower accuracy (R²_CAL = 0.71). Even though an agreement between NIRS and CMA methods was confirmed by a Bland–Altman analysis, confidence limits of agreement differed by up to 25%. Our results support the viability of fecal NIRS analysis to study spatial and temporal variations of the Pyrenean chamois’ diets in summer and winter when differences in the consumption of woody and annual plants are the greatest. This new use for the NIRS technique would be useful to assess the consequences of global change on the feeding behavior of this mountain ungulate and also in other ungulate counterparts.

Genomic variation in the American pika: signatures of geographic isolation and implications for conservation

Background

Distributional responses by alpine taxa to repeated, glacial-interglacial cycles throughout the last two million years have significantly influenced the spatial genetic structure of populations. These effects have been exacerbated for the American pika (Ochotona princeps), a small alpine lagomorph constrained by thermal sensitivity and a limited dispersal capacity. As a species of conservation concern, long-term lack of gene flow has important consequences for landscape genetic structure and levels of diversity within populations. Here, we use reduced representation sequencing (ddRADseq) to provide a genome-wide perspective on patterns of genetic variation across pika populations representing distinct subspecies. To investigate how landscape and environmental features shape genetic variation, we collected genetic samples from distinct geographic regions as well as across finer spatial scales in two geographically proximate mountain ranges of eastern Nevada.

Results

Our genome-wide analyses corroborate range-wide, mitochondrial subspecific designations and reveal pronounced fine-scale population structure between the Ruby Mountains and East Humboldt Range of eastern Nevada. Populations in Nevada were characterized by low genetic diversity (π = 0.0006–0.0009; θ_W = 0.0005–0.0007) relative to populations in California (π = 0.0014–0.0019; θ_W = 0.0011–0.0017) and the Rocky Mountains (π = 0.0025–0.0027; θ_W = 0.0021–0.0024), indicating substantial genetic drift in these isolated populations. Tajima’s D was positive for all sites (D = 0.240–0.811), consistent with recent contraction in population sizes range-wide.

Conclusions

Substantial influences of geography, elevation and climate variables on genetic differentiation were also detected and may interact with the regional effects of anthropogenic climate change to force the loss of unique genetic lineages through continued population extirpations in the Great Basin and Sierra Nevada.

Development of a Panel of Genotyping-in-Thousands by Sequencing in Capsicum

Genotyping by sequencing (GBS) enables genotyping of multiple loci at low cost. However, the single nucleotide polymorphisms (SNPs) revealed by GBS tend to be randomly distributed between individuals, limiting their direct comparisons without applying the various filter options to obtain a comparable dataset of SNPs. Here, we developed a panel of a multiplex targeted sequencing method, genotyping-in-thousands by sequencing (GT-seq), to genotype SNPs in Capsicum spp. Previously developed Fluidigm^® SNP markers were converted to GT-seq markers and combined with new GT-seq markers developed using SNP information obtained through GBS. We then optimized multiplex PCR conditions: we obtained the highest genotyping rate when the first PCR consisted of 25 cycles. In addition, we determined that 101 primer pairs performed best when amplifying target sequences of 79 bp. We minimized interference of multiplex PCR by primer dimer formation using the PrimerPooler program. Using our GT-seq pipeline on Illumina Miseq and Nextseq platforms, we genotyped up to 1,500 (Miseq) and 1,300 (Nextseq) samples for the optimum panel size of 100 loci. To allow the genotyping of Capsicum species, we designed 332 informative GT-seq markers from Fluidigm SNP markers and GBS-derived SNPs. This study illustrates the first application of GT-seq in crop plants. The GT-seq marker set developed here will be a useful tool for molecular breeding of peppers in the future.

Experimental study of hypoxia-induced changes in gene expression in an Asian pika, Ochotona dauurica

Acclimation to environmental changes driven by alterations in gene expression will serve as an important response for some species facing rapid Anthropogenic climate change. Pikas, genus Ochotona, are particularly vulnerable to climate change and current trends suggest that only the highest, coldest elevations within their ranges may remain suitable habitat for these species. In this study we aimed to assess the role of changes in gene expression in potentially facilitating elevational movements in pikas by measuring gene expression in the only known captive pika population, Ochotona dauurica, in response to hypoxic conditions. Using a controlled experiment, we exposed four male pikas to oxygen concentrations characteristic of sea-level, 2,000 m, and 4,000 m for 5 days each. Using blood samples collected after each treatment, we used RNAseq to determine if candidate pathways were undergoing significant changes in gene expression at different levels of oxygen (~100%, ~77%, and ~61% of sea-level oxygen concentrations). Gene set enrichment analyses showed that gene sets associated with the oxidative phosphorylation pathway and electron transport chain were significantly enriched for up-regulated genes in the 4,000 m samples compared to samples from the same individuals at lower-elevation conditions. Up-regulation of these pathways is consistent with known mechanisms of oxygen compensation. Our results suggest that these pikas have the acclimation capacity to tolerate oxygen concentrations characteristic of any elevation within their species range and that gene expression can be changed in a matter of days to accommodate drastically different oxygen concentrations. Thus, rapid and radical elevational movements that may be required of some pika species to avoid warmer temperatures in the Anthropocene will likely not be limited by hypoxic stress.

Contamination and risk assessment of heavy metals, and uranium of sediments in two watersheds in Abiete-Toko gold district, Southern Cameroon

In this investigation, the level of toxic metals (Cd, Pb, Hg, Cu, Ni, Al, Zn and U) was determined in sediment samples from two watersheds (Kienké and Tchangué) in the Abiete-Toko gold district, southern Cameroon. The potential contamination and toxicity of studied metals was determined by evaluating enrichment factor (EF), geo-accumulation index (Igeo) and ecological risk assessment (ERA). Considering the spatial distribution patterns, metal concentrations were lower than the average shale values, except for Cu and Ni of site 4 in the Kienké watershed and only Ni in the Tchangué watershed. In this study, the EF and Igeo values revealed that sediments were moderately polluted by Ni and Cu and unpolluted by other metals. The evaluation of the ERA based on ecological risk index (RI), ecological risk factor (Er), contamination factor (CF) and pollution load index (PLI) revealed that the sediments from the Abiete-Toko watersheds have significant to very high ecological risk assessment and are generally unpolluted by trace metals and U, except for Ni and Cu. Little quantities of heavy metals with low U levels and distribution were found at the sites close to the vicinity of artisanal mining and peri-urban areas. This proximity reveals that artisanal gold mining activities, agricultural runoff, and other anthropogenic inputs in the study area are probable sources of slight metal contamination. However, the non-use of toxic effluents for gold mining and pesticides for agriculture can be an advantage of the unpolluted status of the watersheds. The physical degradation of the ecosystem through excavations, wells and other stream diversion methods is expanding in the zone. Appropriate measures should be taken by artisans to rehabilitate the gold mining sites, to ensure appropriate treatment of wastewater and non-use of toxic effluents into nearby tributaries.

Noninvasive sampling reveals population genetic structure in the Royle's pika, Ochotona roylei, in the western Himalaya

Understanding population genetic structure of climate-sensitive herbivore species is important as it provides useful insights on how shifts in environmental conditions can alter their distribution and abundance. Herbivore responses to the environment can have a strong indirect cascading effect on community structure. This is particularly important for Royle's pika (Lagomorpha: Ochotona roylei), a herbivorous talus-dwelling species in alpine ecosystem, which forms a major prey base for many carnivores in the Himalayan arc. In this study, we used seven polymorphic microsatellite loci to detect evidence for recent changes in genetic diversity and population structure in Royle's pika across five locations sampled between 8 and 160 km apart in the western Himalaya. Using four clustering approaches, we found the presence of significant contemporary genetic structure in Royle's pika populations. The detected genetic structure could be primarily attributed to the landscape features in alpine habitat (e.g., wide lowland valleys, rivers) that may act as semipermeable barriers to gene flow and distribution of food plants, which are key determinants in spatial distribution of herbivores. Pika showed low inbreeding coefficients (F IS) and a high level of pairwise relatedness for individuals within 1 km suggesting low dispersal abilities of talus-dwelling pikas. We have found evidence of a recent population bottleneck, possibly due to effects of environmental disturbances (e.g., snow melting patterns or thermal stress). Our results reveal significant evidence of isolation by distance in genetic differentiation (F ST range = 0.04-0.19). This is the first population genetics study on Royle's pika, which helps to address evolutionary consequences of climate change which are expected to significantly affect the distribution and population dynamics in this talus-dwelling species.

A diet rich in C3 plants reveals the sensitivity of an alpine mammal to climate change

Plant-herbivore interactions provide critical insights into the mechanisms that govern the spatiotemporal distributions of organisms. These interactions are crucial to understanding the impacts of climate change, which are likely to have an effect on the population dynamics of alpine herbivores. The Royle's pika (Ochotona roylei, hereafter pika) is a lagomorph found in the western Himalaya and is dependent on alpine plants that are at risk from climate change. As the main prey of many carnivores in the region, the pika plays a crucial role in trophic interactions. We examined topographical features, plant genera presence and seasonal dynamics as drivers of the plant richness in the pika's diet across an elevational gradient (2,600-4,450 m). We identified 79 plant genera in the faecal pellets of pikas, of which 89% were forbs, >60% were endemic to the Himalaya, and 97.5% of the diet plant genera identified followed the C3 photosynthetic pathway. We found that, during the premonsoon season, the number of genera in the pika's diet decreased with increasing elevation. We demonstrate that a large area of talus supports greater plant diversity and, not surprisingly, results in higher species richness in the pika's diet. However, in talus habitat with deep crevices, pikas consumed fewer plant genera suggesting they may be foraging suboptimally due to predation risk. The continued increase in global temperature is expected to have an effect on the distribution dynamics of C3 plants and consequently influence pika diet and distribution, resulting in a significant negative cascading effect on the Himalayan ecosystem.