Soil Micro-eukaryotic Diversity Patterns Along Elevation Gradient Are Best Estimated by Increasing the Number of Elevation Steps Rather than Within Elevation Band Replication.

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. In studies of elevational diversity pattern, a trade-off is choosing between replication within elevation bands vs. sampling more elevation bands. We addressed this question for soil protists along an elevation gradient on Mt. Asahi, Hokkaido, Japan. We compared two sampling approaches: (1) the replicate strategy (five replicates at six elevational bands, total = 30) and (2) the transect strategy (one sample in each of 16 different elevational bands). Despite a nearly twofold lower sampling effort, the transect strategy yielded congruent results compared to the replicate strategy for the estimation of elevational alpha diversity pattern: the regression coefficients between diversity indices and elevation did not differ between the two options. Furthermore, for a given total number of samples, gamma diversity estimated across the entire transect was higher when sampling more elevational bands as compared to replication from fewer elevational bands. Beta diversity (community composition turnover) was lower within a given elevational band than between adjacent bands and increased with elevation distance. In redundancy analyses, soil organic matter-related variable (the first principal component of soil organic matter, water content, total organic carbon, and nitrogen by whom were highly correlated) and elevation best explained elevational beta diversity pattern for both sampling approaches. Taken together, our results suggest that sampling a single plot per elevation band will be sufficient to obtain a good estimate of soil micro-eukaryotic diversity patterns along elevation gradients. This study demonstrated the effectiveness of the transect strategy in estimating diversity patterns along elevation gradients which is instructive for future environmental or even experimental studies. While not advocating for completely replacing replication-based sampling practices, it is important to note that both replicate and transect strategies have their merits and can be employed based on specific research goals and resource limitations.

Tree-ring analysis and modeling approaches yield contrary response of circumboreal forest productivity to climate change.

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 this study, we investigated the sensitivity of forest productivity to climate change using ring width indices (RWI) from a tree-ring width dataset accessed from the International Tree-Ring Data Bank and gridded climate datasets from the Climate Research Unit. A negative relationship of RWI with summer temperature and recent reductions in RWI were typically observed in continental dry regions, such as inner Alaska and Canada, southern Europe, and the southern part of eastern Siberia. We then developed a multiple regression model with regional meteorological parameters to predict RWI, and then applied to these models to predict how tree growth will respond to twenty-first-century climate change (RCP8.5 scenario). The projections showed a spatial variation and future continuous reduction in tree growth in those continental dry regions. The spatial variation, however, could not be reproduced by a dynamic global vegetation model (DGVM). The DGVM projected a generally positive trend in future tree growth all over the circumboreal region. These results indicate that DGVMs may overestimate future wood net primary productivity (NPP) in continental dry regions such as these; this seems to be common feature of current DGVMs. DGVMs should be able to express the negative effect of warming on tree growth, so that they simulate the observed recent reduction in tree growth in continental dry regions.

A new species of the genus Calotes (Squamata: Agamidae) from high elevations of the Knuckles massif of Sri Lanka.

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 Günther, 1872 which has an isolated population in the central highlands and is only known from Pundaluoya (~1000m), Dickoya (~1200m), Upcot (~1400m), Agrapatanas (1665m) and Peak Wilderness (Sri Pada) (>1400m). The populations from Pundaluoya and Dickoya appear to be locally extinct from the wild and are known only from museum specimens collected over 120 years ago. Males of the new species are different from males of C. liocephalus because of the absence of a gular pouch; by having mid gular scales smaller in size than those of its counterpart; scales on the snout which are larger in size than those on the occipital and forehead; pectoral scales which are not enlarged; elongated subcaudal scales; slightly carinate and acuminate abdominal scales; and scales on venter which are somewhat larger in size than those on dorsum at the same level. Finally, we also redescribe Calotes liocephalus, and provide a key to the Sri Lankan species of genus Calotes.

Soil filtration-sedimentation improves shelled protist recovery in eukaryotic eDNA surveys.

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 has not yet been tested. In this study, we evaluated the effect of a 150 µm mesh size filtration and sedimentation method to improve the recovery of protist eDNA, while reducing the co-extraction of plant, animal and fungal eDNA, using a set of contrasted forest and alpine soils from La Réunion, Japan, Spain and Switzerland. Total eukaryotic diversity was estimated by V4 18S rRNA metabarcoding and classical amplicon sequence variant calling. A 2- to 3-fold enrichment in shelled protists (Euglyphida, Arcellinida and Chrysophyceae) was observed at the sample level with the proposed method, with, at the same time, a 2-fold depletion of Fungi and a 3-fold depletion of Embryophyceae. Protist alpha diversity was slightly lower in filtered samples due to reduced coverage in Variosea and Sarcomonadea, but significant differences were observed in only one region. Beta diversity varied mostly between regions and habitats, which explained the same proportion of variance in bulk soil and filtered samples. The increased resolution in soil protist diversity estimates provided by the filtration-sedimentation method is a strong argument in favour of including it in the standard protocol for soil protist eDNA metabarcoding studies.

Multiple drivers of the COVID-19 spread: The roles of climate, international mobility, and region-specific conditions.

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 (relative amounts of international visitors) in shaping the geographical patterns of COVID-19 case numbers across 1,020 countries/regions, and examined the sequential shift that occurred from December 2019 to June 30, 2020 in multiple drivers of the cumulative number of COVID-19 cases. Our regression model adequately explains the cumulative COVID-19 case numbers (per 1 million population). As the COVID-19 spread progressed, the explanatory power (R2) of the model increased, reaching > 70% in April 2020. Climate, host mobility, and host susceptibility to COVID-19 largely explained the variance among COVID-19 case numbers across locations; the relative importance of host mobility and that of host susceptibility to COVID-19 were both greater than that of climate. Notably, the relative importance of these factors changed over time; the number of days from outbreak onset drove COVID-19 spread in the early stage, then human mobility accelerated the pandemic, and lastly climate (temperature) propelled the phase following disease expansion. Our findings demonstrate that the COVID-19 pandemic is deterministically driven by climate suitability, cross-border human mobility, and region-specific COVID-19 susceptibility. The identification of these multiple drivers of the COVID-19 outbreak trajectory, based on mapping the spread of COVID-19, will contribute to a better understanding of the COVID-19 disease transmission risk and inform long-term preventative measures against this disease.

Integrating multiple sources of ecological data to unveil macroscale species abundance.

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 hierarchical modelling approach to estimate macroscale patterns of species abundance. Using this approach, estimates of absolute abundance of 1248 woody plant species at a 10-km-grid-square resolution over East Asian islands across subtropical to temperate biomes are obtained. We provide two examples of the basic and applied use of the estimated species abundance for (1) inference of macroevolutionary processes underpinning regional biodiversity patterns and (2) quantitative community-wide assessment of a national red list. These results highlight the potential of the elucidation of macroscale species abundance that has thus far been an inaccessible but critical property of biodiversity.

Factors determining forest diversity and biomass on a tropical volcano, Mt. Rinjani, Lombok, Indonesia.

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 modeled alpha- (plot) and beta- (among plot) diversity (Fisher's alpha), compositional change, and biomass against elevation and selected covariates. We also examined community phylogenetic structure across the elevational gradient. We recorded 902 trees and shrubs among 92 species, and 67 species of ground-cover plants. For understorey, subcanopy and canopy plants, an increase in elevation was associated with a decline in alpha-diversity, whereas data for ground-cover plants suggested a hump-shaped pattern. Elevation was consistently the most important factor in determining alpha-diversity for all components. The alpha-diversity of ground-cover vegetation was also negatively correlated with leaf area index, which suggests low light conditions in the understorey may limit diversity at lower elevations. Beta-diversity increased with elevation for ground-cover plants and declined at higher elevations for other components of the vegetation. However, statistical power was low and we could not resolve the relative importance to beta-diversity of different factors. Multivariate GLMs of variation in community composition among plots explained 67.05%, 27.63%, 18.24%, and 19.80% of the variation (deviance) for ground-cover, understorey, subcanopy and canopy plants, respectively, and demonstrated that elevation was a consistently important factor in determining community composition. Above-ground biomass showed no significant pattern with elevation and was also not significantly associated with alpha-diversity. At lower elevations communities had a random phylogenetic structure, but from 1600 m communities were phylogenetically clustered. This suggests a greater role of environmental filtering at higher elevations, and thus provides a possible explanation for the observed decline in diversity with elevation.

Wild pigs (Sus scrofa) mediate large-scale edge effects in a lowland tropical rainforest in Peninsular Malaysia.

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 lowland rain forest. To investigate this hypothesis, we established three 1 km transects from the forest/Oil Palm plantation boundary into the forest interior. We recorded the distribution of soil disturbance by wild pigs, C. hirta abundance, and environmental variables. These data were analyzed using a hierarchical Bayesian model that incorporated spatial auto-correlation in the environmental variables. As predicted, soil disturbance by wild pigs declined with distance from forest edge and C. hirta abundance was correlated with the level of soil disturbance. Importantly there was no effect of distance on C. hirta abundance, after controlling for the effect of soil disturbance. Clidemia hirta abundance was also correlated with the presence of canopy openings, but there was no significant association between the occurrence of canopy openings and distance from the edge. Increased levels of soil disturbance and C. hirta abundance were still detectable approximately 1 km from the edge, demonstrating the potential for exceptionally large-scale animal mediated edge effects.