A semi-automatic workflow to process images from small mammal camera traps

Camera traps have become popular for monitoring biodiversity, but the huge amounts of image data that arise from camera trap monitoring represent a challenge and artificial intelligence is increasingly used to automatically classify large image data sets. However, it is still challenging to combine automatic classification with other steps and tools needed for efficient, quality-assured and adaptive processing of camera trap images in long-term monitoring programs. Here we propose a semi-automatic workflow to process images from small mammal cameras that combines all necessary steps from downloading camera trap images in the field to a quality checked data set ready to be used in ecological analyses. The workflow is implemented in R and includes (1) managing raw images, (2) automatic image classification, (3) quality check of automatic image labels, as well as the possibilities to (4) retrain the model with new images and to (5) manually review subsets of images to correct image labels. We illustrate the application of this workflow for the development of a new monitoring program of an Arctic small mammal community. We first trained a classification model for the specific small mammal community based on images from an initial set of camera traps. As the monitoring program evolved, the classification model was retrained with a small subset of images from new camera traps. This case study highlights the importance of model retraining in adaptive monitoring programs based on camera traps as this step in the workflow increases model performance and substantially decreases the total time needed for manually reviewing images and correcting image labels. We provide all R scripts to make the workflow accessible to other ecologists

Long-term herbivore removal experiments reveal how geese and reindeer shape vegetation and ecosystem CO2-fluxes in high-Arctic tundra

1. Given the current rates of climate change, with associated shifts in herbivore population densities, understanding the role of different herbivores in ecosystem functioning is critical for predicting ecosystem responses. Here, we examined how migratory geese and resident, non-migratory reindeer—two dominating yet functionally contrasting herbivores—control vegetation and ecosystem processes in rapidly warming Arctic tundra. 2. We collected vegetation and ecosystem carbon (C) flux data at peak plant growing season in the two longest running, fully replicated herbivore removal experiments found in high-Arctic Svalbard. Experiments had been set up independently in wet habitat utilised by barnacle geese Branta leucopsis in summer and in moist-to-dry habitat utilised by wild reindeer Rangifer tarandus platyrhynchus year-round. 3. Excluding geese induced vegetation state transitions from heavily grazed, mossdominated (only 4 g m−2 of live above-ground vascular plant biomass) to ungrazed, graminoid-dominated (60 g m−2 after 4-year exclusion) and horsetail-dominated (150 g m−2 after 15-year exclusion) tundra. This caused large increases in vegetation C and nitrogen (N) pools, dead biomass and moss-layer depth. Alterations in plant N concentration and CN ratio suggest overall slower plant community nutrient dynamics in the short-term (4-year) absence of geese. Long-term (15-year) goose removal quadrupled net ecosystem C sequestration (NEE) by increasing ecosystem photosynthesis more than ecosystem respiration (ER). 4. Excluding reindeer for 21 years also produced detectable increases in live aboveground vascular plant biomass (from 50 to 80 g m−2; without promoting vegetation state shifts), as well as in vegetation C and N pools, dead biomass, moss-layer depth and ER. Yet, reindeer removal did not alter the chemistry of plants and soil or NEE. 5. Synthesis. Although both herbivores were key drivers of ecosystem structure and function, the control exerted by geese in their main habitat (wet tundra) was much more pronounced than that exerted by reindeer in their main habitat (moist-todry tundra). Importantly, these herbivore effects are scale dependent, because geese are more spatially concentrated and thereby affect a smaller portion of the tundra landscape compared to reindeer. Our results highlight the substantial heterogeneity in how herbivores shape tundra vegetation and ecosystem processes, with implications for ongoing environmental change

Beratung als Instrument für mehr Naturschutz in der Landwirtschaft : Evaluierung des Beratungsangebotes im Verbundprojekt „Rotmilan – Land zum Leben“

From 2014 to 2018, within the scope of the "Rotmilan – Land zum Leben" joint project, more than 880 farms were given advice on the implementation of red-kite-friendly agriculture in eight regions of Germany. The main objective was to improve food availability for red kites on agricul-tural land. During the entire project period, it was possible to increase the area where measures were applied, from approx. 1,000 ha to more than 13,000 ha/year. Following an initial evaluation by Schmidt und Breitsameter (2015) on the advice given to farmers, the consultants and farm representatives – including those that did not receive any advice – were interviewed on their experiences and perspectives. The focus was on the motivation to participate in the counselling and its effects, as well as the expectations for nature conservation counselling. In summary, the following six core statements can be derived from the results: (1) Suitable funding programmes are a prerequisite for target-oriented implementation of nature conservation measures on agricultural land. (2) Advisory services promote the implementation of measures by attracting new farms to partic-ipate and increasing the amount of land involved. (3) Long-term and constant advisory services offered enable the continuous acquisition of new farms and the development of trust and cooperation. (4) Practical support in the implementation of measures, follow-up advice and the communica-tion of successful measures by the advisory institution are important components of the advisory activity. (5) Region-specific features of the advisory services are derived from the available funding measures, the characteristics of the advisory institution and advisors as well as the agricultural structure. (6) Advisory support promotes the quality of the implemented measures, thus the success of the measures cannot be measured solely on the basis of the area covered by the measures. The study reveals that advising farmers is an important instrument for the implementation of nature conservation measures. Advice transfers nature conservation expertise into land man-agement and sensitises the actors. Moreover, it offers support during the implementation of measures. The basics requirements for an effective advisory service, however, are sufficiently financed means for measures, adapted to both region-specific biodiversity targets and agricultur-al requirements

One leaf for all: Chemical traits of single leaves measured at the leaf surface using near-infrared reflectance spectroscopy

1. The leaf is an essential unit for measures of plant ecological traits. Yet, measures of plant chemical traits are often achieved by merging several leaves, masking potential foliar variation within and among plant individuals. This is also the case with cost‐effective measures derived using near‐infrared reflectance spectroscopy (NIRS). The calibration models developed for converting NIRS spectral information to chemical traits are typically based on spectra from merged and milled leaves. In this study, we ask whether such calibration models can be applied to spectra derived from whole leaves, providing measures of chemical traits of single leaves. 2. We sampled cohorts of single leaves from different biogeographic regions, growth forms, species and phenological stages to include variation in leaf and chemical traits. For each cohort, we first sampled NIRS spectra from each whole, single leaf, including leaf sizes down to Ø 4 mm (the minimum area of our NIRS application). Next, we merged, milled and tableted the leaves and sampled spectra from the cohort as a tablet. We applied arctic–alpine calibration models to all spectra and derived chemical traits. Finally, we evaluated the performance of the models in predicting chemical traits of whole, single leaves by comparing the traits derived at the level of leaves to that of the tablets. 3. We found that the arctic–alpine calibration models can successfully be applied to single, whole leaves for measures of nitrogen (R2 = 0.88, RMSE = 0.824), phosphorus (R2 = 0.65, RMSE = 0.081) and carbon (R2 = 0.78, RMSE = 2.199) content. For silicon content, we found the method acceptable when applied to silicon‐rich growth forms (R2 = 0.67, RMSE = 0.677). We found a considerable variation in chemical trait values among leaves within the cohorts. 4. This time‐ and cost‐efficient NIRS application provides non‐destructive measures of a set of chemical traits in single, whole leaves, including leaves of small sizes. The application can facilitate research into the scales of variability of chemical traits and include intra‐individual variation. Potential trade‐offs among chemical traits and other traits within the leaf unit can be identified and be related to ecological processes. In sum, this NIRS application can facilitate further ecological understanding of the role of leaf chemical traits

Herbivory and warming have opposing short-term effects on plant-community nutrient levels across high-Arctic tundra habitats

Environmental changes can rapidly alter standing biomass in tundra plant communities; yet, to what extent can they modify plant-community nutrient levels? Nutrient levels and their changes can affect biomass production, nutrient cycling rates and nutrient availability to herbivores. We examined how environmental perturbations alter Arctic plant-community leaf nutrient concentrations (percentage of dry mass, i.e. resource quality) and nutrient pools (absolute mass per unit area, i.e. resource quantity). We experimentally imposed two different types of environmental perturbations in a high-Arctic ecosystem in Svalbard, spanning three habitats differing in soil moisture and plant-community composition. We mimicked both a pulse perturbation (a grubbing event by geese in spring) and a press perturbation (a constant level of summer warming). After 2 years of perturbations, we quantified peak-season nitrogen and phosphorus concentrations in 1268 leaf samples from the most abundant vascular plant species. We derived community-weighted nutrient concentrations and total amount of nutrients (pools) for whole plant communities and individual plant functional types (PFTs). Spring grubbing increased plant-community nutrient concentrations in mesic (+13%) and wet (+8%), but not moist, habitats, and reduced nutrient pools in all habitats (moist: −49%; wet, mesic: −31% to −37%). Conversely, summer warming reduced plant-community nutrient concentrations in mesic and moist (−10% to −12%), but not wet, habitats and increased nutrient pools in moist habitats (+50%). Fast-growing PFTs exhibited nutrient-concentration responses, while slow-growing PFTs generally did not. Grubbing enhanced nutrient concentrations of forbs and grasses in wet habitats (+20%) and of horsetails and grasses in mesic habitats (+19–23%). Conversely, warming decreased nutrient concentrations of horsetails in wet habitats (−15%) and of grasses, horsetails and forbs in moist habitats (−12% to −15%). Nutrient pools held by each PFT were less affected, although the most abundant PFTs responded to perturbations. Synthesis. Arctic plant-community nutrient levels can be rapidly altered by environmental changes, with consequences for short-term process rates and plant-herbivore interactions. Community-level responses in nutrient concentrations and pools were opposing and differed among habitats and PFTs. Our findings have implications for how we understand herbivory- and warming-induced shifts in the fine-scaled distribution of resource quality and quantity within and across tundra habitats

Ny nasjonal smågnagerovervåking i fjell basert på kamerafeller. Forslag til innsamlingsdesign og dataprosessering

Kleiven, E.F., Framstad, E., Bakkestuen, V., Böhner, H., Cretois, B., Frassinelli, F., Ims, R.A., Jepsen, J.U., Soininen, E.M. & Eide, N.E. 2022. Ny nasjonal smågnagerovervåking i fjell basert på kamerafeller. Forslag til innsamlingsdesign og dataprosessering. NINA Rapport 2170. Norsk institutt for naturforskning. Denne rapporten presenterer et forslag til et nytt nasjonalt overvåkingsprogram for smågnagere i fjell basert på kamerafeller. Utredningen er bestilt av Miljødirektoratet. Overordnet målsetting for overvåkingsprogrammet er å bidra med data til smågnagerindikatoren i fagsystemet for økologisk tilstand i fjell. Programmet skal så langt mulig, dekke variasjonen i regionale og lokale klimaforhold, samt andre naturgitte forhold, for å kunne vurdere effekter av påvirkningsfaktorer dersom det oppstår endringer i smågnagerbestandene over tid. Resultater fra programmet skal kunne brukes i vurderingen av bevaringstiltak for fjellrev, snøugle og dverggås. Ny nasjonal smågnagerovervåking foreslås basert på vel 50 lokaliteter som dekker alle sentrale fjellområder og et utvalg av mer perifere fjellområder i øst, vest og langs kysten. Disse lokalitetene vil gi bestandsdata for smågnagere som tilfredsstiller alle formålene med overvåkingsprogrammet. Lokalitetene er videre prioritert ut fra hvor godt de dekker overvåkingsformålene og i hvilken grad det allerede finnes dataserier for lokale smågnagerbestander i nærheten. Tolv lokaliteter med prioritet I dekker i hovedsak sentrale fjellområder fra sør til nord, viktige områder for fjellrev og har eksisterende dataserier for smågnagere. Seksten lokaliteter med prioritet II supplere de foregående, spesielt ved å dekke større deler av klimagradienten fra oseaniske til kontinentale områder. Tjuefem lokaliteter med prioritet III utfyller de foregående ved å øke dekningen av ulike fjellområder. Endelig plassering av lokalitetene må vurderes etter feltbefaring. Innen hver overvåkningslokalitet foreslås et romlig hierarkisk overvåkningsdesign. På lokalitetsnivå bør overvåkningen dekke de sentrale habitatene (lynghei, tuemark, snøleier) for de viktigste smågnagerartene i fjell: gråsidemus, lemen, markmus/fjellmarkmus. Samtidig bør både lav- og mellomalpin sone dekkes. Innen hvert habitat og hver klimasone anbefales seks kamerafeller (romlige replikater), dvs. i alt 36 kamerafeller pr. lokalitet. Dette vil med stor sannsynlighet være tilstrekkelig til å få en god indeks for bestandsstørrelse for alle de viktige smågnagerartene for hvert habitat og klimasone innen hver overvåkningslokalitet, selv med noe datatap som følge av tekniske feil. Den fulle versjonen av overvåkingsprogrammet bør omfatte de aller fleste av de foreslåtte lokalitetene. Noen få lokaliteter som anses å dekke marginale fjellområder kan ev. utelates. For en nedskalert versjon av overvåkingen anbefales å bruke alle lokaliteter med prioritet I eller II. En minimumsversjon av overvåkingen bør omfatte lokalitetene med prioritet I, ev. supplert med noen med prioritet II som er mest relevante for arbeidet med å bevare fjellrev. I utgangspunktet foreslås ingen reduksjon av overvåkingsdesignet pr. lokalitet, men det anbefales en evaluering av programmet etter fem års drift, for å vurdere om det er forsvarlig å redusere antall kamerafeller pr. lokalitet. Andre initiativer som kan gi supplerende informasjon om utbredelsen av smågnagertopper, er gjennomgått og vurdert. Det vil kreve nærmere vurdering av disse initiativenes observasjonsinnsats og metoder for å kunne vurdere nytten av slik informasjon for det foreslåtte overvåkingsprogrammet. I rapporten beskrives fullstendig arbeidsflyt fra innhenting av minnekort til et ferdig kvalitetssikret og tilgjengeliggjort datasettsett med bestandsindeks for ulike smågnagere. Denne arbeidsflyten kombinerer maskinlæring for automatisk bildeklassifisering med manuell kontroll av utvalgte bilder. Det vil i oppstarten være behov for tilrettelegging av treningsdata til utvikling av en ny maskinlæringsmodell, samt kvalitetssikring av modellklassifiseringene. Overvåkingsprogrammet bør koordineres av en faginstitusjon som støttes av et bredere faglig råd. Driften av programmet i felt bør i størst mulig grad koordineres med eksisterende feltapparat (f.eks. SNO) for å oppnå både logistiske og faglige synergier med andre overvåkingsprogrammer. Det er videre estimert en budsjettramme for de tre alternative overvåkingsoppleggene, full versjon, nedskalert versjon og minimumsversjon. Noe utviklingsarbeid vil kreves i oppstarten av programmet. Det er fremfor alt store investeringskostnader knyttet til kamerainnkjøp, deretter kostnader til årlig drift varierende fra litt under 2,5 millioner i en minimumsversjon til nesten 11 millioner i full versjon.Kleiven, E.F., Framstad, E., Bakkestuen, V., Böhner, H., Cretois, B., Frassinelli, F., Ims, R.A., Jepsen, J.U., Soininen, E.M. & Eide, N.E. 2022. New national monitoring of small rodents in Norwegian Arctic and Alpine tundrabased on camera traps. Proposed sampling design and data processing. NINA Report 2170. Norwegian Institute for Nature Research. This report presents a proposal for a new national monitoring program for small rodents in mountains, based on camera traps. The report was commissioned by the Norwegian Environment Agency. The overall objective of the monitoring programme is to contribute data to the small rodent indicator for the assessment of ecological condition in tundra ecosystems. The programme shall, as far as possible, cover variations in regional and local climate conditions, as well as other natural conditions, to assess the effects of impact factors on possible changes in small rodent populations over time. Results from the programme can also be used in the assessment of conservation measures for Arctic foxes, snowy owls and lesser white-fronted geese. The new national small rodent monitoring is proposed to be based on over 50 sites covering all central mountain areas and a selection of more peripheral alpine areas in the east, west and along the coast. These sites will provide population data for small rodents that satisfy all the objectives of the monitoring programme. The sites are also prioritised based on how well they cover the monitoring objectives and whether data series for small rodent populations are available in the vicinity. Twelve priority I sites mainly cover central alpine areas from the south to alpine and Arctic areas in the north, important areas for Arctic foxes and have existing data series for small rodents. Sixteen priority II sites supplement the previous ones, particularly by covering larger parts of the climate gradient from oceanic to continental areas. The twenty-five priority III sites further increase the coverage of various mountainous areas. The final location of the sites must be considered after field inspection. Within each site, a spatial hierarchical monitoring design is proposed. At the site level, monitoring should cover the central habitats (heathlands, tussocks, snow beds) for the main small rodent species in Norwegian tundra ecosystems (grey-sided vole Myodes rufocanus, Norwegian lemming Lemmus lemmus, field vole Microtus agrestis and tundra vole Microtus oeconomus). Both the low and middle alpine zones should be covered. Within each habitat and climate zone, six camera traps (spatial replicas) are recommended, i.e., a total of 36 camera traps per site. This will most likely be sufficient to obtain a good population size index for all important small rodent species for each habitat and climate zone within each monitoring site, even with some data loss due to technical malfunction. The full version of the monitoring programme should include most of the proposed sites. A few sites considered to cover marginal mountain areas may be omitted. A scaled-down version of the monitoring should include all sites of priority I or II. A minimum version should include sites of priority I, possibly supplemented by some of priority II that are most relevant for conservation of Arctic foxes. Initially, no reduction in the monitoring design per site is proposed, but an evaluation of the program after five years of operation is recommended to assess whether it is prudent to reduce the number of camera traps per site. Other initiatives that may provide supplementary information on the distribution of small rodent peaks have been reviewed and assessed. Further assessment of these initiatives' observation efforts and methods will be required to assess the benefits of such information for the proposed monitoring programme. The report describes the complete workflow from collecting memory cards to a ready-made quality-assured and accessible dataset set with abundance indexes for various small rodent species. This workflow combines machine learning for automatic image classification with manual control of selected images. Initially, adaptation of training data for the development of a new machine learning model will be needed, as well as quality assurance of the model classifications. The monitoring programme should be coordinated by a research institution supported by a broader scientific council. The field operation of the programme should as far as possible be coordinated with existing field activities (e.g., by the Norwegian Nature Inspectorate), to achieve both logistical and scientific synergies with other monitoring programmes. An overall budget has been estimated for the three alternative monitoring schemes, the full version, the scaled-down version, and the minimum version. Some development work will be required at the start of the programme. Initial costs associated with camera procurement are particularly large, followed by annual operation costs varying from just under 2.5 million NOK in a minimum version to almost 11 million NOK in full version