Classifying organisms and artefacts by their outline shapes

We often wish to classify objects by their shapes. Indeed, the study of shapes is an important part of many scientific fields, such as evolutionary biology, structural biology, image processing and archaeology. However, mathematical shape spaces are rather complicated and nonlinear. The most widely used methods of shape analysis, geometric morphometrics, treat the shapes as sets of points. Diffeomorphic methods consider the underlying curve rather than points, but have rarely been applied to real-world problems. Using a machine classifier, we tested the ability of several of these methods to describe and classify the shapes of a variety of organic and man-made objects. We find that one method, based on square-root velocity functions (SRVFs), outperforms all others, including a standard geometric morphometric method (eigenshapes), and that it is also superior to human experts using shape alone. When the SRVF approach is constrained to take account of homologous landmarks it can accurately classify objects of very different shapes. The SRVF method identifies a shortest path between shapes, and we show that this can be used to estimate the shapes of intermediate steps in evolutionary series. Diffeomorphic shape analysis methods, we conclude, now provide practical and effective solutions to many shape description and classification problems in the natural and human sciences.</p

Global transpiration data from sap flow measurements : the SAPFLUXNET database

Plant transpiration links physiological responses of vegetation to water supply and demand with hydrological, energy, and carbon budgets at the land-atmosphere interface. However, despite being the main land evaporative flux at the global scale, transpiration and its response to environmental drivers are currently not well constrained by observations. Here we introduce the first global compilation of whole-plant transpiration data from sap flow measurements (SAPFLUXNET, https://sapfluxnet.creaf.cat/, last access: 8 June 2021). We harmonized and quality-controlled individual datasets supplied by contributors worldwide in a semi-automatic data workflow implemented in the R programming language. Datasets include sub-daily time series of sap flow and hydrometeorological drivers for one or more growing seasons, as well as metadata on the stand characteristics, plant attributes, and technical details of the measurements. SAPFLUXNET contains 202 globally distributed datasets with sap flow time series for 2714 plants, mostly trees, of 174 species. SAPFLUXNET has a broad bioclimatic coverage, with woodland/shrubland and temperate forest biomes especially well represented (80 % of the datasets). The measurements cover a wide variety of stand structural characteristics and plant sizes. The datasets encompass the period between 1995 and 2018, with 50 % of the datasets being at least 3 years long. Accompanying radiation and vapour pressure deficit data are available for most of the datasets, while on-site soil water content is available for 56 % of the datasets. Many datasets contain data for species that make up 90 % or more of the total stand basal area, allowing the estimation of stand transpiration in diverse ecological settings. SAPFLUXNET adds to existing plant trait datasets, ecosystem flux networks, and remote sensing products to help increase our understanding of plant water use, plant responses to drought, and ecohydrological processes. SAPFLUXNET version 0.1.5 is freely available from the Zenodo repository (https://doi.org/10.5281/zenodo.3971689; Poyatos et al., 2020a). The "sapfluxnetr" R package - designed to access, visualize, and process SAPFLUXNET data - is available from CRAN.Peer reviewe

Termite sensitivity to temperature affects global wood decay rates.

Deadwood is a large global carbon store with its store size partially determined by biotic decay. Microbial wood decay rates are known to respond to changing temperature and precipitation. Termites are also important decomposers in the tropics but are less well studied. An understanding of their climate sensitivities is needed to estimate climate change effects on wood carbon pools. Using data from 133 sites spanning six continents, we found that termite wood discovery and consumption were highly sensitive to temperature (with decay increasing >6.8 times per 10°C increase in temperature)-even more so than microbes. Termite decay effects were greatest in tropical seasonal forests, tropical savannas, and subtropical deserts. With tropicalization (i.e., warming shifts to tropical climates), termite wood decay will likely increase as termites access more of Earth's surface

Soil CO2 efflux in an old-growth southern conifer forest

This is the research data set underlying the article "Soil CO₂ efflux in an old-growth southern conifer forest (<i>Agathis australis</i>) – magnitude, components, and controls" which is published in the journal SOIL (doi:10.5194/soil-2016-21).<br><br>Total soil CO₂ efflux, autotrophic and heterotrophic respiration, and soil data was measured in the University of Auckland Huapai reserve as part of a research project on carbon cycling in an old-growth kauri forest. Measurements were conducted between August 2012 and January 2014. <br><br><br

The use of pre-dawn leaf water potential and MODIS LAI to explore seasonal trends in the phenology of Australian and southern African woodlands and savannas

Trends in global soil moisture are needed to inform models of soil-plant-atmosphere interactions. Predawn leaf water potential (Ψpd), a surrogate for soil moisture and an index of plant water stress, has been routinely collected in Australian forests, woodlands and savannas, but the associated leaf area index (LAI) has seldom been available to enable the preparation of a Ψpd on LAI relationship. Following an analysis of Ψpd and MODIS LAI data from Australian forests, woodlands and savannas, we identified patterns in Ψpd which provide an understanding of the role of soil-moisture status in controlling LAI. In the savanna of northern Australia, the MODIS LAI product had a basal value of 0.96 during the dry season as compared with a mean value of 2.5 for the wet season. The dry season value is equivalent to the LAI of the tree component and corresponds with ground-truthed LAI. Ψpd is lowest (more negative) during the height of the dry season (late October) at -2.5 MPa, and highest (-0.1 MPa) during the wet season (early March). We present two models which predict Ψpd from the MODIS LAI product. These may be useful surrogates for studying trends in soil moisture in highly seasonal climates and may contribute to climate change research

Beyond yield and toward sustainability : Using applied ecology to support biodiversity conservation and food production

Agroecological research has an important role in supporting evidence‐based land management to ensure food production is achieved whilst minimising the impacts on biodiversity and its associated ecosystem processes and services. This nexus between often competing priorities of optimal production and sustainability requires greater knowledge of management decisions to enact more sustainable and transformative practice change and to better conserve biodiversity. We highlight three key knowledge gaps in this area: (i) The use of appropriate indicators to measure dependencies and impacts on biodiversity; (ii) Methods to improve the management of resources to support the “health” of biodiversity within agroecosystems; (iii) Greater understanding of the ecosystem processes, and services generated and received across terrestrial and aquatic habitats. Synthesis and applications. Ecological research and robust science will play a vital role in supporting more sustainable food production. We see Journal of Applied Ecology playing a key role in promoting agricultural research that goes beyond a narrow focus on increasing output, and encourage more submissions at the interface of agriculture, ecology and biodiversity conservation, considering social and economic aspects for a sustainable future

Exploring the Influence of Biological Traits and Environmental Drivers on Water Use Variations across Contrasting Forests

Understanding species-specific water use patterns across contrasting sites and how sensitivity of responses to environmental variables changes for different species is critical for evaluating potential forest dynamics and land use changes under global change. To quantify water use patterns and the sensitivity of tree transpiration to environmental drivers among sites and species, sap flow and meteorological data sets from three contrasting climatic zones were combined and compared in this analysis. Agathis australis from NZHP site, Schima wallichii Choisy (native) and Acacia mangium Willd (exotic) from CHS site, Liquidamber formosana Hance, Quercus variabilis Blume and Quercus acutissima Carruth from CJGS site were the dominant trees chosen as our study species. Biological traits were collected to explain the underlying physiological mechanisms for water use variation. Results showed that the strongest environmental drivers of sap flow were photosynthetically active radiation (PAR), vapor pressure deficit (VPD) and temperature across sites, indicating that the response of water use to abiotic drivers converged across sites. Water use magnitude was site specific, which was controlled by site characteristics, species composition and local weather conditions. The species with higher sap flow density (Fd) generally had greater stomatal conductance. Native deciduous broadleaved species had a higher Fd and faster response to stomatal regulation than that of native evergreen broadleaved species (S. wallichii) and conifer species A. australis. The analysis also showed that exotic species (A. mangium) consumed more water than native species (S. wallichii). Trees with diffuse porous and lower wood density had relatively higher Fd for angiosperms, suggesting that water use was regulated by physiological differences. Water use characteristics across sites are controlled by both external factors such as site-specific characteristics (local environmental conditions and species composition) and internal factors such as biological traits (xylem anatomy, root biomass and leaf area), which highlights the complexity of quantifying land water budgets for areas covered by different species

A synthesis of tree functional traits related to drought-induced mortality in forests across climatic zones

1. Forest dieback caused by drought-induced tree mortality has been observed world-wide. Forecasting which trees in which locations are vulnerable to drought-induced mortality is important to predict the consequences of drought on forest structure, biodiversity and ecosystem function. 2. In this paper, our central aim was to compile a synthesis of tree traits and associated abiotic variables that can be used to predict drought-induced mortality. We reviewed the literature that specifically links drought mortality to functional traits and site conditions (i.e. edaphic variables and biotic conditions), targeting studies that show clear use of tree traits in drought analysis. We separated the review into five climatic zones to determine global vs. regionally restricted relationships between traits and mortality. 3. Our synthesis identifies a number of traits that have clear relationships with drought-induced mortality (e.g. wood density at the species level and tree size and growth at the individual level). However, the lack of direct relationships between most traits and drought-induced mortality highlights areas where future research should focus to broaden our understanding. 5. Synthesis and applications. Our synthesis highlights established relationships between traits and drought-induced mortality, presents knowledge gaps for future research focus and suggests monitoring and research avenues for improving our understanding of drought-induced mortality. It is intended to assist ecologists and natural resource managers choose appropriate and measurable parameters for predicting local and regional scale tree mortality risk in different climatic zones within constraints of time and funding availability