A simple survey protocol for assessing terrestrial biodiversity in a broad range of ecosystems

A comparative mapping of plant species diversity using ensemble learning algorithms combined with high accuracy surface modeling

Plant species diversity (PSD) has always been an essential component of biodiversity and plays an important role in ecosystem functions and services. However, it is still a huge challenge to simulate the spatial distribution of PSD due to the difficulties of data acquisition and unsatisfactory performance of predicting algorithms over large areas. A surge in the number of remote sensing imagery, along with the great success of machine learning, opens new opportunities for the mapping of PSD. Therefore, different machine learning algorithms combined with high-accuracy surface modeling (HASM) were firstly proposed to predict the PSD in the Xinghai, northeastern Qinghai-Tibetan Plateau, China. Spectral reflectance and vegetation indices, generated from Landsat 8 images, and environmental variables were taken as the potential explanatory factors of machine learning models including least absolute shrinkage and selection operator (Lasso), ridge regression (Ridge), eXtreme Gradient Boosting (XGBoost), and Random Forest (RF). The prediction generated from these machine learning methods and in situ observation data were integrated by using HASM for the high-accuracy mapping of PSD including three species diversity indices. The results showed that PSD was closely associated with vegetation indices, followed by spectral reflectance and environmental factors. XGBoost combined with HASM (HASM-XGBoost) showed the best performance with the lowest MAE and RMSE. Our results suggested that the fusion of heterogeneous data and the ensemble of heterogeneous models may revolutionize our ability to predict the PSD over large areas, especially in some places limited by sparse field samples.

Tree species identity and composition shape the epiphytic lichen community of structurally simple boreal forests over vast areas

Greatly simplified ecosystems are often neglected for biodiversity studies. However, these simplified systems dominate in many regions of the world, and a lack of understanding of what shapes species occurrence in these systems can have consequences for biodiversity and ecosystem services at a massive scale. In Fennoscandia, ~90% of the boreal forest (~21Mha) is structurally simplified with little knowledge of how forest structural elements shape the occurrence and diversity of for example epiphytic lichens in these managed forests. One form of structural simplification is the reduction of the number and frequency of different tree species. As many lichen species have host tree preferences, it is particularly likely that this simplification has a huge effect on the lichen community in managed forests. In a 40–70 years old boreal forest in Sweden, we therefore related the occurrence and richness of all observed epiphytic lichens to the host tree species and beta and gamma lichen diversity at the forest stand level to the stand’s tree species composition and stem diameter. Picea abies hosted the highest lichen richness followed by Pinus sylvestris, Quercus robur, Alnus glutinosa, Betula spp., and Populus tremula. However, P. tremula hosted twice as many uncommon species as any of the other tree species. Stand level beta and gamma diversity was twice as high on stands with four compared to one tree species, and was highest when either coniferous or deciduous trees made up 40–50% of the trees. The stem diameter was positively related to lichen richness at the tree and stand level, but negatively to beta diversity. For biodiversity, these findings imply that leaving a few trees of a different species during forest thinning is unlikely as effective as combining life-boat trees for endangered species with an even tree species mixture.

Polypore fungi as a flagship group to indicate changes in biodiversity - a test case from Estonia

Polyporous fungi, a morphologically delineated group of Agaricomycetes (Basidiomycota), are considered well studied in Europe and used as model group in ecological studies and for conservation. Such broad interest, including widespread sampling and DNA based taxonomic revisions, is rapidly transforming our basic understanding of polypore diversity and natural history. We integrated over 40,000 historical and modern records of polypores in Estonia (hemiboreal Europe), revealing 227 species, and including Polyporus submelanopus and P. ulleungus as novelties for Europe. Taxonomic and conservation problems were distinguished for 13 unresolved subgroups. The estimated species pool exceeds 260 species in Estonia, including at least 20 likely undescribed species (here documented as distinct DNA lineages related to accepted species in, e.g., Ceriporia, Coltricia, Physisporinus, Sidera and Sistotrema). Four broad ecological patterns are described: (1) polypore assemblage organization in natural forests follows major soil and tree-composition gradients; (2) landscape-scale polypore diversity homogenizes due to draining of peatland forests and reduction of nemoral broad-leaved trees (wooded meadows and parks buffer the latter); (3) species having parasitic or brown-rot life-strategies are more substrate-specific; and (4) assemblage differences among woody substrates reveal habitat management priorities. Our update reveals extensive overlap of polypore biota throughout North Europe. We estimate that in Estonia, the biota experienced ca. 3-5% species turnover during the twentieth century, but exotic species remain rare and have not attained key functions in natural ecosystems. We encourage new regional syntheses on long studied fungal groups to obtain landscape-scale understanding of species pools, and for elaborating fungal indicators for biodiversity assessments.

A Random Forest Modelling Procedure for a Multi-Sensor Assessment of Tree Species Diversity

Earth observation data can provide important information for tree species diversity mapping and monitoring. The relatively recent advances in remote sensing data characteristics and processing systems elevate the potential of satellite imagery for providing accurate, timely, consistent, and robust spatially explicit estimates of tree species diversity over forest ecosystems. This study was conducted in Northern Pindos National Park, the largest terrestrial park in Greece and aimed to assess the potential of four satellite sensors with different instrumental characteristics, for the estimation of tree diversity. Through field measurements, we originally quantified two diversity indices, namely the Shannon diversity index (H’) and Simpson’s diversity (D1). Random forest regression models were developed for associating remotely sensed spectral signal with tree species diversity within the area. The models generated from the use of the WorldView-2 image were the most accurate with a coefficient of determination of up to 0.44 for H’ and 0.37 for D1. The Sentinel-2 -based models of tree species diversity performed slightly worse, but were better than the Landsat-8 and RapidEye models. The coefficient of variation quantifying internal variability of spectral values within each plot provided little or no usage for improving the modelling accuracy. Our results suggest that very-high-spatial-resolution imagery provides the most important information for the assessment of tree species diversity in heterogeneous Mediterranean ecosystems.

The Potential of Production Forests for Sustaining Lichen Diversity: A Perspective on Sustainable Forest Management

There is a critical gap in our knowledge about sustainable forest management in order to maintain biodiversity with respect to allocating conservation efforts between production forests and set-asides. Field studies on this question are notably scarce on species-rich, poorly detectable taxon groups. On the basis of forest lichen surveys in Estonia, we assessed the following: (i) how much production stands contribute to maintaining the full species pool and (ii) how forest habitat conditions affect this contribution for habitat specialist species. The field material was collected in a “semi-natural forestry” system, which mitigates negative environmental impacts of even-aged forestry and forestry drainage by frequently using natural regeneration, tree retention, and low intensity of thinnings. We performed standard-effort surveys of full assemblages of lichens and allied fungi (such as non-lichenized calicioid and lichenicolous fungi) and measured stand structure in 127 2 ha plots, in mainland Estonia. The plots represented four management stages (old growth, mature preharvest forests, clear-cut sites with retention trees, and clear-cut sites without retention trees). The 369 recorded species represent an estimated 70% of the full species pool studied. Our main finding was that production forests supported over 80% of recorded species, but only one-third appears tolerant of management intensification. The landscape-scale potential of production forests through biodiversity-friendly silviculture is approximately twice as high as the number of tolerant species and, additionally, many very rare species depend on setting aside their scattered localities. The potential is much smaller at the scale of individual stands. The scale effect emerges because multiple stands contribute different sets of sensitive and infrequent species. When the full potential of production forests is realized, the role of reserves is to protect specific old-growth dependent taxa (15% to 20% of the species pool). Our study highlights that production forests form a heterogeneous and dynamic target for addressing the biodiversity conservation principle of sustainable forest management.

Recovery of the Critically Endangered bracket fungus Amylocystis lapponica in the Estonian network of strictly protected forests

In regions where primeval forests have vanished it is unclear whether forest protection can sustain specialized old-forest biota, and over what time scale. We report on population expansion of an old-growth specific fungus of European conservation concern, Amylocystis lapponica, in the forest reserve network of Estonia. This conspicuous species was known for 40 years from only single records in one old-growth forest and was categorized nationally as Critically Endangered. During the last 10 years A. lapponica has expanded over the eastern half of the country, with nine subpopulations, in 12 localities, now known, all in long-protected old-growth forests and several > 50 km apart. In most of the new localities historical absence of the species can be reliably assessed based on earlier surveys. The historical remnant subpopulation has also increased. The population size (c. 100 mature individuals) in Estonia indicates the species should be recategorized nationally as Endangered. This success story suggests that more than 50 years of non-intervention may be needed even in large old-forest reserves for old-growth specialist species to recover.