Species level mapping of a seagrass bed using an unmanned aerial vehicle and deep learning technique.

Background: Seagrass beds are essential habitats in coastal ecosystems, providing valuable ecosystem services, but are threatened by various climate change and human activities. Seagrass monitoring by remote sensing have been conducted over past decades using satellite and aerial images, which have low resolution to analyze changes in the composition of different seagrass species in the meadows. Recently, unmanned aerial vehicles (UAVs) have allowed us to obtain much higher resolution images, which is promising in observing fine-scale changes in seagrass species composition. Furthermore, image processing techniques based on deep learning can be applied to the discrimination of seagrass species that were difficult based only on color variation. In this study, we conducted mapping of a multispecific seagrass bed in Saroma-ko Lagoon, Hokkaido, Japan, and compared the accuracy of the three discrimination methods of seagrass bed areas and species composition, i.e., pixel-based classification, object-based classification, and the application of deep neural network. Methods: We set five benthic classes, two seagrass species (Zostera marina and Z. japonica), brown and green macroalgae, and no vegetation for creating a benthic cover map. High-resolution images by UAV photography enabled us to produce a map at fine scales (<1 cm resolution). Results: The application of a deep neural network successfully classified the two seagrass species. The accuracy of seagrass bed classification was the highest (82%) when the deep neural network was applied. Conclusion: Our results highlighted that a combination of UAV mapping and deep learning could help monitor the spatial extent of seagrass beds and classify their species composition at very fine scales.

Genetic divergence and range expansion in a western North Pacific coral.

Coral poleward range expansions have recently been observed in response to warming oceans. Range expansion can lead to reduced genetic diversity and increased frequency of deleterious mutations that were rare in core populations, potentially limiting the ability for adaptation and persistence in novel environments. Successful expansions that overcome these founder effects and colonize new habitat have been attributed to multiple introductions from different sources, hybridization with native populations, or rapid adaptive evolution. Here, we investigate population genomic patterns of the reef-building coral Acropora hyacinthus along a latitudinal cline that includes a well-established range expansion front in Japan using 2b-RAD sequencing. A total of 184 coral samples were collected across seven sites spanning from ~24°N to near its northern range front at ~33°N. We uncover the presence of three cryptic lineages of A. hyacinthus, which occupy discrete reefs within this region. Only one lineage is present along the expansion front and we find evidence for its historical occupation of marginal habitats. Within this lineage we also find evidence of bottleneck pressures associated with expansion events including higher clonality, increased linkage disequilibrium, and lower genetic diversity in range edge populations compared to core populations. Asymmetric migration between populations was also detected with lower migration from edge sites. Lastly, we describe genomic signatures of local adaptation potentially attributed to lower winter temperatures experienced at the more recently expanded northern populations. Together these data illuminate the genomic consequences of range expansion in a coral and highlight how adaptation to discrete environments along expansion fronts may facilitate further range expansion in this temperate coral lineage.

Estimation of tsunami debris on seafloors towards future disaster preparedness: Unveiling spatial varying effects of combined land use and oceanographic factors.

A large amount of tsunami debris from the Great East Japan Earthquake in 2011 was sunk on the seafloor and threatened the marine ecosystem and local communities' economy, especially in fisheries. However, few studies estimated spatial accumulations of tsunami benthic debris, comparing to their flows on the ocean surface. Here, a spatially varying coefficient model was used to estimate tsunami debris accumulation considering the spatial structure of the data off the Tohoku region. Our model revealed the number of vessels nearest the coast at the tsunami event had the highest positive impact, whereas the distance from the coast and kinetic energy influenced negatively. However, the effect of the proximity to the coast wasn't detected in the Sendai bay, indicating spatial dependency of these effects. Our model estimation provides the fundamental information of tsunami debris accumulation on the seafloor, supporting early reconstruction and risk reduction in marine ecosystems and local communities.

The potential role of temperate Japanese regions as refugia for the coral Acropora hyacinthus in the face of climate change.

As corals in tropical regions are threatened by increasing water temperatures, poleward range expansion of reef-building corals has been observed, and temperate regions are expected to serve as refugia in the face of climate change. To elucidate the important indicators of the sustainability of coral populations, we examined the genetic diversity and connectivity of the common reef-building coral Acropora hyacinthus along the Kuroshio Current, including recently expanded (<50 years) populations. Among the three cryptic lineages found, only one was distributed in temperate regions, which could indicate the presence of Kuroshio-associated larval dispersal barriers between temperate and subtropical regions, as shown by oceanographic simulations as well as differences in environmental factors. The level of genetic diversity gradually decreased towards the edge of the species distribution. This study provides an example of the reduced genetic diversity in recently expanded marginal populations, thus indicating the possible vulnerability of these populations to environmental changes. This finding underpins the importance of assessing the genetic diversity of newly colonized populations associated with climate change for conservation purposes. In addition, this study highlights the importance of pre-existing temperate regions as coral refugia, which has been rather underappreciated in local coastal management.

Disentangling the drivers of invasion spread in a vector-borne tree disease.

Pine wilt disease (PWD) invaded southern Japan in the early 1900s and has gradually expanded its range to northern Honshu (Japanese mainland). The disease is caused by a pathogenic North American nematode, which is transmitted by native pine sawyer beetles. Recently, the disease has invaded other portions of East Asia and Europe where extensive mortality of host pines is anticipated to resemble historical patterns seen in Japan. There is a critical need to identify the main drivers of PWD invasion spread so as to predict the future spread and evaluate containment strategies in newly invaded world regions. But the coupling of pathogen and vector population dynamics introduces considerable complexity that is important for understanding this and other plant disease invasions. In this study, we analysed historical (1980-2011) records of PWD infection and vector abundance, which were spatially extensive but recorded at coarse categorical levels (none, low and high) across 403 municipalities in northern Honshu. We employed a multistate occupancy model that accounted both for demographic stochasticity and observation errors in categorical data. Analysis revealed that sparse sawyer populations had lower probabilities of transition to high abundance than did more abundant populations even when regional abundance stayed the same, suggesting the existence of positive density dependence, that is an Allee effect, in sawyer dynamics. Climatic conditions (average accumulated degree days) substantially limited invasion spread in northern regions, but this climatic influence on sawyer dynamics was generally weaker than the Allee effect. Our results suggest that tactics (eg sanitation logging of infected pines) which strengthen Allee effects in sawyer dynamics may be effective strategies for slowing the spread of PWD.

Landscape heterogeneity-biodiversity relationship: effect of range size.

The importance of landscape heterogeneity to biodiversity may depend on the size of the geographic range of species, which in turn can reflect species traits (such as habitat generalization) and the effects of historical and contemporary land covers. We used nationwide bird survey data from Japan, where heterogeneous landscapes predominate, to test the hypothesis that wide-ranging species are positively associated with landscape heterogeneity in terms of species richness and abundance, whereas narrow-ranging species are positively associated with landscape homogeneity in the form of either open or forest habitats. We used simultaneous autoregressive models to explore the effects of climate, evapotranspiration, and landscape heterogeneity on the richness and abundance of breeding land-bird species. The richness of wide-ranging species and the total species richness were highest in heterogeneous landscapes, where many wide-ranging species showed the highest abundance. In contrast, the richness of narrow-ranging species was not highest in heterogeneous landscapes; most of those species were abundant in either open or forest landscapes. Moreover, in open landscapes, narrow-ranging species increased their species richness with decreasing temperature. These results indicate that heterogeneous landscapes are associated with rich bird diversity but that most narrow-ranging species prefer homogeneous landscapes--particularly open habitats in colder regions, where grasslands have historically predominated. There is a need to reassess the generality of the heterogeneity-biodiversity relationship, with attention to the characteristics of species assemblages determined by environments at large spatiotemporal scales.

Re-structuring of marine communities exposed to environmental change: a global study on the interactive effects of species and functional richness.

Species richness is the most commonly used but controversial biodiversity metric in studies on aspects of community stability such as structural composition or productivity. The apparent ambiguity of theoretical and experimental findings may in part be due to experimental shortcomings and/or heterogeneity of scales and methods in earlier studies. This has led to an urgent call for improved and more realistic experiments. In a series of experiments replicated at a global scale we translocated several hundred marine hard bottom communities to new environments simulating a rapid but moderate environmental change. Subsequently, we measured their rate of compositional change (re-structuring) which in the great majority of cases represented a compositional convergence towards local communities. Re-structuring is driven by mortality of community components (original species) and establishment of new species in the changed environmental context. The rate of this re-structuring was then related to various system properties. We show that availability of free substratum relates negatively while taxon richness relates positively to structural persistence (i.e., no or slow re-structuring). Thus, when faced with environmental change, taxon-rich communities retain their original composition longer than taxon-poor communities. The effect of taxon richness, however, interacts with another aspect of diversity, functional richness. Indeed, taxon richness relates positively to persistence in functionally depauperate communities, but not in functionally diverse communities. The interaction between taxonomic and functional diversity with regard to the behaviour of communities exposed to environmental stress may help understand some of the seemingly contrasting findings of past research.