Molecular dietary analyses of western capercaillies (Tetrao urogallus) reveal a diverse diet

Conservation strategies centered around species habitat protection rely on species’ dietary information. One species at the focal point of conservation efforts is the herbivorous grouse, the western capercaillie (Tetrao urogallus), which is an indicator species for forest biodiversity conservation. Non-molecular means used to study their diet are time-consuming and at low taxonomic resolution. This delays the implementation of conservation strategies including resource protection due to uncertainty about its diet. Thus, limited knowledge on diet is hampering conservation efforts. Here, we use non-invasive environmental DNA (eDNA) metabarcoding on DNA extracted from faces to present the first large-scale molecular dietary analysis of capercaillies. Facal samples were collected from seven populations located in Norway (Finnmark, Troms, Trøndelag, Innlandet) and France (Vosges, Jura, Pyrenees) (n = 172). We detected 122 plant taxa belonging to 46 plant families of which 37.7% of the detected taxa could be identified at species level. The average dietary richness of each sample was 7 ± 5 SD taxa. The most frequently occurring plant groups with the highest relative read abundance (RRA) were trees and dwarf shrubs, in particular, Pinus and Vaccinium myrtillus, respectively. There was a difference in dietary composition (RRA) between samples collected from the different locations (adonis pseudo F5,86 = 11.01, r2 = 0.17, p = 0.001) and seasons (adonis pseudo F2,03 = 0.64, r2 = 0.01, p = 0.036). Dietary composition also differed between sexes at each location (adonis pseudo F1,47 = 2.77, r2 = 0.04, p = 0.024), although not significant for all data combined. In total, 35 taxa (36.8% of taxa recorded) were new capercaillie food items compared with existing knowledge from non-molecular means. The non-invasive molecular dietary analysis applied in this study provides new ecological information of capercaillies’ diet, improving our understanding of adequate habitat required for their conservation

Pollen, macrofossils and sedaDNA reveal climate and land use impacts on Holocene mountain vegetation of the Lepontine Alps, Italy

Both climate change and anthropogenic disturbance affect vegetation composition, but it is difficult to separate these drivers of vegetation change from one another. A better understanding of past vegetation dynamics is necessary to disentangle the influence of different forcing factors and assess future vegetation change. Here we present the first multi-proxy palaeoecological study combining sedimentary ancient DNA (sedaDNA), pollen, spores, stomata, charcoal and plant macrofossils from the Alps. We reconstructed the Holocene vegetation dynamics and fire history at Lago Inferiore del Sangiatto (1980 m asl), a small lake in the subalpine belt of the Ossola region, Italian Lepontine Alps. Afforestation in response to climate warming started at 10,700 cal yr BP with Larix decidua and tree Betula, which formed open forests together with Pinus cembra from 10,500 cal yr BP onwards. Human impact on the regional vegetation started at 5100 cal yr BP, resulting in expansions of Picea abies and Alnus viridis and the collapse of Abies alba. Species response models and ordination analysis show that livestock grazing and fire were major drivers of vegetation change at Lago Inferiore del Sangiatto during the late Holocene. Finally, increasing human impact during the Bronze (ca. 4200e2900 cal yr BP) and Iron Age (ca. 2900 e2000 cal yr BP) led to the formation of species-rich larch meadows and alpine pastures that are still dominant today. The palaeoecological data suggest that under projected climate change and land abandonment, the treeline ecotone will likely shift to higher altitudes, leading to important changes in species composition and increasing the risk of biodiversity loss

High-throughput sequencing of African chikanda cake highlights conservation challenges in orchids

Source at https://doi.org/10.1007/s10531-017-1343-7 .Chikanda is a traditional dish made with wild-harvested ground orchid tubers belonging to three orchidioid genera, Disa, Satyrium and Habenaria, all of which are CITES appendix II-listed. Identification of collected orchid tubers is very difficult and documentation of constituent species in prepared chikanda has hitherto been impossible. Here amplicon metabarcoding was used in samples of six prepared chikanda cakes to study genetic sequence diversity and species diversity in this product. Molecular operational taxonomic unit identification using similarity-matching reveals that species of all three genera were present in the chikanda samples studied. Disa was present in all of the samples, Satyrium in five out of six and Habenaria in one of the samples, as well as a number of other plants. The fact that each sample contained orchids and the presence of a wide variety of species from all genera in this traditional dish raise serious concerns about the sustainability of this trade and the future of wild orchid populations in the main harvest areas. This proof-of-concept study shows that Ion-Torrent PGM is a cost-effective scalable platform for metabarcoding using the relatively long nrITS1 and nrITS2 regions. Furthermore, nrITS metabarcoding can be successfully used for the detection of specific ingredients in a highly-processed food product at genus level, and this makes it a useful tool in the detection of possible conservation issues arising from commercialized trade or processed plant products

Clitellate worms (Annelida) in late-glacial and Holocene sedimentary DNA records from the Polar Urals and northern Norway

While there are extensive macro‐ and microfossil records of a range of plants and animals from the Quaternary, earthworms and their close relatives amongst annelids are not preserved as fossils and therefore the knowledge of their past distributions is limited. This lack of fossils means that clitellate worms (Annelida) are currently underused in palaeoecological research, even though they can provide valuable information about terrestrial and aquatic environmental conditions. Their DNA might be preserved in sediments, which offers an alternative method for detection. Here we analyse lacustrine sediments from lakes in the Polar Urals, Arctic Russia, covering the period 24 000–1300 cal. a BP, and NE Norway, covering 10 700–3300 cal. a BP, using a universal mammal 16S rDNA marker. While mammals were recorded using the marker (reindeer was detected twice in the Polar Urals core at 23 000 and 14 000 cal. a BP, and four times in the Norwegian core at 11 000 cal. a BP and between 3600–3300 cal. a BP), worm extracellular DNA ‘bycatch’ was rather high. In this paper we present the first reported worm detection from ancient DNA. Our results demonstrate that both aquatic and terrestrial clitellates can be identified in late‐Quaternary lacustrine sediments, and the ecological information retrievable from this group warrants further research with a more targeted approach.publishedVersio

Holocene floristic diversity and richness in northeast Norway revealed by sedimentary ancient DNA (sedaDNA) and pollen

Source at https://doi.org/10.1111/bor.12357We present a Holocene record of floristic diversity and environmental change for the central Varanger Peninsula, Finnmark, based on ancient DNA extracted from the sediments of a small lake (sedaDNA). The record covers the period c. 10 700 to 3300 cal. a BP and is complemented by pollen data. Measures of species richness, sample evenness and beta diversity were calculated based on sedaDNA sampling intervals and 1000‐year time windows. We identified 101 vascular plant and 17 bryophyte taxa, a high proportion (86%) of which are still growing within the region today. The high species richness (>60 taxa) observed in the Early Holocene, including representatives from all important plant functional groups, shows that modern shrub‐tundra communities, and much of their species complement, were in place as early as c. 10 700 cal. a BP. We infer that postglacial colonization of the area occurred prior to the full Holocene, during the Pleistocene‐Holocene transition, Younger Dryas stadial or earlier. Abundant DNA of the extra‐limital aquatic plant Callitriche hermaphroditica suggests it expanded its range northward between c. 10 200 and 9600 cal. a BP, when summers were warmer than present. High values of Pinus DNA occur throughout the record, but we cannot say with certainty if they represent prior local presence; however, pollen influx values >500 grains cm−2 a−1 between c. 8000 and 7300 cal. a BP strongly suggest the presence of pine woodland during this period. As the site lies beyond the modern tree limit of pine, it is likely that this expansion also reflects a response to warmer Early Holocene summers

The treasure vault can be opened: large-scale genome skimming works well using herbarium and silica gel dried material

Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications

Enriched biodiversity data as a resource and service

Background: Recent years have seen a surge in projects that produce large volumes of structured, machine-readable biodiversity data. To make these data amenable to processing by generic, open source “data enrichment” workflows, they are increasingly being represented in a variety of standards-compliant interchange formats. Here, we report on an initiative in which software developers and taxonomists came together to address the challenges and highlight the opportunities in the enrichment of such biodiversity data by engaging in intensive, collaborative software development: The Biodiversity Data Enrichment Hackathon. Results: The hackathon brought together 37 participants (including developers and taxonomists, i.e. scientific professionals that gather, identify, name and classify species) from 10 countries: Belgium, Bulgaria, Canada, Finland, Germany, Italy, the Netherlands, New Zealand, the UK, and the US. The participants brought expertise in processing structured data, text mining, development of ontologies, digital identification keys, geographic information systems, niche modeling, natural language processing, provenance annotation, semantic integration, taxonomic name resolution, web service interfaces, workflow tools and visualisation. Most use cases and exemplar data were provided by taxonomists. One goal of the meeting was to facilitate re-use and enhancement of biodiversity knowledge by a broad range of stakeholders, such as taxonomists, systematists, ecologists, niche modelers, informaticians and ontologists. The suggested use cases resulted in nine breakout groups addressing three main themes: i) mobilising heritage biodiversity knowledge; ii) formalising and linking concepts; and iii) addressing interoperability between service platforms. Another goal was to further foster a community of experts in biodiversity informatics and to build human links between research projects and institutions, in response to recent calls to further such integration in this research domain. Conclusions: Beyond deriving prototype solutions for each use case, areas of inadequacy were discussed and are being pursued further. It was striking how many possible applications for biodiversity data there were and how quickly solutions could be put together when the normal constraints to collaboration were broken down for a week. Conversely, mobilising biodiversity knowledge from their silos in heritage literature and natural history collections will continue to require formalisation of the concepts (and the links between them) that define the research domain, as well as increased interoperability between the software platforms that operate on these concepts

Postglacial species arrival and diversity buildup of northern ecosystems took millennia

What drives ecosystem buildup, diversity, and stability? We assess species arrival and ecosystem changes across 16 millennia by combining regional-scale plant sedimentary ancient DNA from Fennoscandia with near-complete DNA and trait databases. We show that postglacial arrival time varies within and between plant growth forms. Further, arrival times were mainly predicted by adaptation to temperature, disturbance, and light. Major break points in ecological trait diversity were seen between 13.9 and 10.8 calibrated thousand years before the present (cal ka BP), as well as break point in functional diversity at 12.0 cal ka BP, shifting from a state of ecosystem buildup to a state where most habitat types and biotic ecosystem components were in place. Trait and functional diversity stabilized around 8 cal ka BP, after which both remained stable, although changes in climate took place and species inflow continued. Our ecosystem reconstruction indicates a millennial-scale time phase of formation to reach stable and resilient levels of diversity and functioning.publishedVersio

Sedimentary ancient DNA shows terrestrial plant richness continuously increased over the Holocene in northern Fennoscandia

The effects of climate change on species richness are debated but can be informed by the past. Here, we generated a sedimentary ancient DNA dataset covering 10 lakes and applied novel methods for data harmonization. We assessed the impact of Holocene climate changes and nutrients on terrestrial plant richness in northern Fennoscandia. We find that richness increased steeply during the rapidly warming Early Holocene. In contrast to findings from most pollen studies, we show that richness continued to increase thereafter, although the climate was stable, with richness and the regional species pool only stabilizing during the past three millennia. Furthermore, overall increases in richness were greater in catchments with higher soil nutrient availability. We suggest that richness will increase with ongoing warming, especially at localities with high nutrient availability and assuming that human activity remains low in the region, although lags of millennia may be expected.The effects of climate change on species richness are debated but can be informed by the past. Here, we generated a sedimentary ancient DNA dataset covering 10 lakes and applied novel methods for data harmonization. We assessed the impact of Holocene climate changes and nutrients on terrestrial plant richness in northern Fennoscandia. We find that richness increased steeply during the rapidly warming Early Holocene. In contrast to findings from most pollen studies, we show that richness continued to increase thereafter, although the climate was stable, with richness and the regional species pool only stabilizing during the past three millennia. Furthermore, overall increases in richness were greater in catchments with higher soil nutrient availability. We suggest that richness will increase with ongoing warming, especially at localities with high nutrient availability and assuming that human activity remains low in the region, although lags of millennia may be expected.Peer reviewe

High resolution ancient sedimentary DNA shows that alpine plant diversity is associated with human land use and climate change.

The European Alps are highly rich in species, but their future may be threatened by ongoing changes in human land use and climate. Here, we reconstructed vegetation, temperature, human impact and livestock over the past ~12,000 years from Lake Sulsseewli, based on sedimentary ancient plant and mammal DNA, pollen, spores, chironomids, and microcharcoal. We assembled a highly-complete local DNA reference library (PhyloAlps, 3923 plant taxa), and used this to obtain an exceptionally rich sedaDNA record of 366 plant taxa. Vegetation mainly responded to climate during the early Holocene, while human activity had an additional influence on vegetation from 6 ka onwards. Land-use shifted from episodic grazing during the Neolithic and Bronze Age to agropastoralism in the Middle Ages. Associated human deforestation allowed the coexistence of plant species typically found at different elevational belts, leading to levels of plant richness that characterise the current high diversity of this region. Our findings indicate a positive association between low intensity agropastoral activities and precipitation with the maintenance of the unique subalpine and alpine plant diversity of the European Alps