Junichi Fujinuma

University of Tartu · Department of Botany

Dark diversity includes ecologically suitable species currently absent in a site, albeit theoretically able to arrive from the surrounding region. Various methods can estimate the likelihood that an absent species is in the dark diversity of a site. Recent developments in estimation of dark diversity have advanced the field, yet uncertainty on meth...

The development of high-throughput sequencing (HTS) of environmental DNA (eDNA) has stimulated the study of soil microbial diversity patterns and drivers at all scales. However, given the heterogeneity of soils, a challenge is to define effective and efficient sampling protocols that allow sound comparison with other records, especially vegetation....

A large part of the soil protist diversity is missed in metabarcoding studies based on 0.25 g of soil environmental DNA (eDNA) and universal primers due to ca. 80% co-amplification of non-target plants, animals and fungi. To overcome this problem, enrichment of the substrate used for eDNA extraction is an easily implemented option but its effect ha...

Locally observed biodiversity always consists of only a fraction of its site‐specific species pool. Why some suitable species are absent, shaping dark diversity of that site, is a basic yet increasingly crucial question in the face of global biodiversity degradation. The ultimate processes underlying dark diversity associate with either dispersal o...

A large part of the soil protist diversity is missed in metabarcoding studies based on 0.25 g of soil environmental DNA (eDNA) and universal primers due to ca. 80 % co-amplification of non-target plants, animals and fungi. To overcome this problem, enrichment of the substrate used for eDNA extraction is an easyly implemented option but its effect h...

Aim Non‐native species threaten ecosystems worldwide, but we poorly know why some species invade more. Functional traits, residence time and native range size have been often used as invasion predictors. Here, we advance in the field by linking invasion success to native range parameters derived from dark diversity – a set of species present in the...

Following its initial appearance in December 2019, coronavirus disease 2019 (COVID-19) quickly spread around the globe. Here, we evaluated the role of climate (temperature and precipitation), region-specific COVID-19 susceptibility (BCG vaccination factors, malaria incidence, and percentage of the population aged over 65 years), and human mobility...

The novel Coronavirus Disease 2019 (COVID-19) has spread quickly across the globe. Here, we evaluated the role of climate (temperature and precipitation), region-specific susceptibility (BCG vaccination, malaria infection, and elderly population) and international traveller population (human mobility) in shaping the geographical patterns of COVID-1...

The pattern of species abundance, represented by the number of individuals per species within an ecological community, is one of the fundamental characteristics of biodiversity. However, despite their obvious significance in ecology and biogeography, there is still no clear understanding of these patterns at large spatial scales. Here, we develop a...

Plant clonality is a ubiquitous trait observed in many phylogenetic clades and vegetations across tropical to arctic biomes. However, there is no consensus regarding determinant factors of species clonality; especially in the context of species assembly processes, ecological/evolutionary drivers of clonal growth remain largely unknown. To elucidate...

Evolutionary processes underpin the biodiversity on the planet. Theories advocate that the form of the species abundance distribution (SAD), presented by the number of individuals for each species within an ecological community, is intimately linked to speciation modes such as point mutation and random fission. This prediction has rarely been, howe...

Tropical bamboos persist in a wide range of light conditions and quickly respond to changes in light availability. However, the mechanisms underpinning this ability remain unknown. In order to test the hypothesis that the modular and hollow culm architecture of bamboos explains their performance in a wide range of light environments, we determined...

We describe the physiological responses of boreal conifers to climate change for the past 112 years using ring width and carbon isotope ratios (δ13C) chronologies at six forest sites in northern Eurasia and Canada. Responses differed among regions, depending on their climatic and/or geographic characteristics. Tree radial growth decreased over the...

Circumboreal forest ecosystems are exposed to a larger magnitude of warming in comparison with the global average, as a result of warming-induced environmental changes. However, it is not clear how tree growth in these ecosystems responds to these changes. In the present study, we investigated the sensitivity of forest productivity to climate chang...

Systematic conservation planning (SCP) provides a decision-support framework for biodiversity conservation for multistakeholder deliberation. The core concept for designing protected area (PA) networks is the CAR principle, which comprises Comprehensiveness, Adequacy, and Representativeness. This is the basis of conservation planning, involving the...

A new species of agamid lizard, of the genus Calotes, is described based on morphological evidence. This species is restricted to the Knuckles massif (>900 m elevation) of Sri Lanka. The genus Calotes consists of seven species in Sri Lanka, five of which appear to form an endemic radiation. The new species most closely resembles C. liocephalus Günt...

Tropical volcanoes are an important but understudied ecosystem, and the relationships between plant species diversity and compositional change and elevation may differ from mountains created by uplift, because of their younger and more homogeneous soils. We sampled vegetation over an altitudinal gradient on Mt. Rinjani, Lombok, Indonesia. We modele...

Data available from the Dryad Digital Repository: doi:10.5061/dryad.8n6t5 Tropical volcanoes are an important but understudied ecosystem, and the relationships between plant species diversity and compositional change and elevation may differ from mountains created by uplift, because of their younger and more homogeneous soils. We sampled vegetatio...

Summary of models for alpha and beta-diversity of different components of vegetation on Mount Rinjani, Indonesia. Models were arranged according to ΔAIC value. Variables included in the models were elevation, LAI, slope and their respective interactive terms. EL = elevation, SL = slope, LAI = leaf area index. (DOCX)

Non- metric multidimensional scaling (NMDS) ordination of ground-cover plant assemblages on Mount Rinjani, Indonesia. The contours show different elevations and the letters represent different species (the identity of each letter is found in Table S2). (TIF)

Non- metric multidimensional scaling (NMDS) ordination of understorey plant assemblages on Mount Rinjani, Indonesia. The contours show different elevations and the letters represent different species (the identity of each letter is found in Table S2). (TIF)

Non- metric multidimensional scaling (NMDS) ordination of subcanopy plant assemblages on Mount Rinjani, Indonesia. The contours show different elevations and the letters represent different species (the identity of each letter is found in Table S2). (TIF)

Overall species found at Rinjani's plots. G = ground stratum, U = understory stratum, S = subcanopy, and C = canopy. (DOCX)

Summary of models examined for above ground biomass of vegetation on Mt Rinjani. Models are arranged according to ΔAIC value. K refers to numbers of parameters included. EL = elevation and SL = slope. We included elevation and slope in the maximal model (all stations 2200 m included). (DOCX)

Non- metric multidimensional scaling (NMDS) ordination of canopy plant assemblages on Mount Rinjani, Indonesia. The contours show different elevations and the letters represent different species (the identity of each letter is found in Table S2). (TIF)

Edge-effects greatly extend the area of tropical forests degraded through human activities. At Pasoh, Peninsular Malaysia, it has been suggested that soil disturbance by highly abundant wild pigs (Sus scrofa), which feed in adjacent Oil Palm plantations, may have mediated the invasion of Clidemia hirta (Melastomataceae) into the diverse tropical lo...

Prior probability distributions used in our hierarchical Bayesian model. The symbols in the left-most column correspond to those used in the model (see Methods section, Text S1). k subscript refers to the transect number. (PDF)

Results of the estimated posterior distributions from our hierarchical Bayesian model. The symbols in left-most column correspond to those used in the model (see Methods section, Text S1). Significant parameters, whose 95% credible interval does not incorporate zero, are in bold. (PDF)

WinBUGS code for the analysis of Clidemia hirta abundance and soil disturbance by Wild pigs. (PDF)