Our recent Methods in Ecology and Evolution paper – ‘Imaging biological surface topography in situ and in vivo‘ – shows how to use gel-based profilometry to image various biological surfaces. To start you need to press a gel into a surface of interest. The bottom surface of the gel is coated in a paint to create an impression of the surface that has standard optical properties (not clear, shiny, or coloured). Then lights are shone on the gel at different angles and photographs are taken at six different lighting angles. These photographs allow us to study the surface in incredible detail. The following images give more information on how we can do this and the benefits of it.
Our first picture shows the peduncle and tail of a yellow perch (Perca flavescens) being pressed into a gel. We use a gel-based profilometry system manufactured by GelSight Inc. (http://www.gelsight.com/). Image: Dylan Wainwright.
The six greyscale photographs in this image are of the scales from the Hawaiian dascyllus (Dascyllus albisella). Each image has a different lighting angle and all six will be used to reconstruct the surface topography on this patch of scales. Imaging a surface is as fast as positioning the specimen and taking six photographs. No specimen preparation is required – this method can be done on clear, shiny, wet, and slimy surfaces! Images: Dylan Wainwright and the Freshwater and Marine Image Bank.
In this picture you can see the surface topography of Dascyllus albisella, reconstructed from the six greyscale images in the previous image. This image captures the lateral line, visible at the top of the image as a row of scales connected by a canal. Heights on this surface are shown as colours: the warmer the colours (oranges and reds), the higher the heights. The height range of this surface is just over 200 microns – the highest parts of the surface are over 200 microns higher than the lowest . Images: Dylan Wainwright and the Freshwater and Marine Image Bank.
Each reconstructed surface is made up of over 18 million three-dimensional points (x, y, and z). This allows for a substantial amount of digital zoom with the ability to still recover surface features. Above is an enlarged view of the posterior margin of a scale from Dascyllus albisella from the same image as the previous two slides. The posterior margin of this scale is made of ctenii, which are small interlocking spines that are present on the scales of many species of fish. Those at the margin are the longest and newest, with older ctenii becoming shortened and serving as a scaffold to interlock with newer ones. Images: Dylan Wainwright and the Freshwater and Marine Image Bank.
The three-dimensional topography data recovered by gel-based profilometry can help you make unique observations on the surface texture of biological surfaces, such as the armor-like ganoid scales of Polypterus endlicheri (see ‘Materials design principles of ancient fish armour’ by Bruet et al. http://go.nature.com/2ivXi8I for more information on poylpterus armor). Using software for surface analysis, height profile lines can be generated (shown above), along with a variety of roughness and surface measurements (not shown). This topographic data is crucial for understanding how biological surfaces interact with their environments. Images: Dylan Wainwright and George Albert Boulenger.
With gel-based profilometry, you can tune the gel properties to match even very soft surfaces, such as the epidermis and mucus that covers the scales of live fish. Above, we show a bluegill (Lepomis macrochirus) that was imaged with and without mucus. Without mucus, many surface details of scales are obvious, such as the concentric growth lines of each scale, the lateral line, and clear margins made of spiny ctenii. When mucus is present, the surface details are obscured. Below each image we provide tables of common surface parameters including root-mean-square roughness (Sq – http://bit.ly/2Amhpeb), kurtosis (Sku – http://bit.ly/2zUY8ne), and skew (Ssk – http://bit.ly/2zUY8ne). Roughness is much lower on the surface with mucus, demonstrating its smoothing effect. This smoothing effect and the material properties of mucus will likely affect the swimming performance of this fish, and these results show how useful this technique can be for exploring surfaces of live animals. Images: Dylan Wainwright and the Freshwater and Marine Image Bank.
Gel-based profilometry is non-invasive and only needs pressure to be applied to the surface of interest to get the image. Above is the surface topography of the back of a human hand. The pores are evident as small blue regions with low elevation. Long flexible structures like hairs will be pressed flat by the sampling gel, as seen in the hairs above. Image: Dylan Wainwright.
You can see the surface of a Boston fern (Nephrolepis exaltata) above. This image was taken at high magnification and then cropped to a 1 mm by 1 mm square. Stomata with guard cells are visible on the surface of the leaf as ring-shaped cells. Images: Dylan Wainwright and Marija Gajić (http://bit.ly/2AxryHp).
This is the forewing of a dragonfly. The wing venation pattern is obvious using this technique, and small spines are present on many of the veins, especially the distal veins towards the wing tip. We produced this image without any special preparation of the subject and without damaging these delicate wings. Images: Dylan Wainwright and Wellcome Library, London (http://bit.ly/2AkcT1J).
The above image shows a dorsal patch of skin from the Chinese crocodile lizard (Shinisaurus crocodilurus). This lizard is an endangered semiaquatic species with skin similar in appearance to a crocodiles (as its name suggests). Gel-based profilometry provides a non-destructive way of investigating the skin morphology of this species using museum specimens. Images: Dylan Wainwright and spacebirdy (CC-BY-SA-3.0) (http://bit.ly/2jCtvb4).
Above we have both a greyscale image and a height map from the hand of a Sulawesi lined gliding lizard (Draco splinotus). For two or one-dimensional measurements, greyscale images can be valuable because of their high contrast. Gel-based profilometry produces grayscale images at a range of sizes, comparable to low to medium magnification scanning electron microscopy. Images: Dylan Wainwright and A.S.Kono (http://bit.ly/2BCFY6W).
The denticles from the lateral flank of a leopard shark (Triakis semifasciata) were imaged and you can see the topographic reconstruction above. Denticles have been shown to increase swimming performance and understanding their surface topography is crucial for connecting the form of shark denticles to hydrodynamic function (see ‘The hydrodynamic function of shark skin and two biomimetic applications’ by Oeffner and Lauder, for example). Images: Dylan Wainwright and Tom Hilton (http://bit.ly/2BpW3vv).
This image shows the skin texture of the white marlin. Although most fish only have one type of bony structure in their skin (scales), white marlin have two. The first are larger, teardrop shaped scales with forked ends that are embedded in the dermis – they’re visible as larger impressions above. The second bony structure present on white marline skin are smaller peaks that are attached to the skin surface and look like small grains in the images above. Understanding these structures is an important step to understanding the function of marlin skin and the reasons behind these modifications (for more information on these scales see ‘Comparative morphology of the scales of roundscale spearfish Tetrapturus georgii and white marlin Kajikia albida’ by Loose et al. – http://bit.ly/2Bq5UBM). Images: Dylan Wainwright and public domain image.
Technological advancements in the past 20 years or so have spurred rapid growth in the study of migratory connectivity (the linkage of individuals and populations between seasons of the annual cycle). A new article in Methods in Ecology and Evolution provides methods to help make quantitative comparisons of migratory connectivity across studies, data types, and taxa to better understand the causes and consequences of the seasonal distributions of populations.
In a new Methods in Ecology and Evolution video, Javier Puy outlines a new method of experimental plant DNA demethylation for ecological epigenetic experiments. While the traditionally-used approach causes underdeveloped root systems and high mortality of treated plants, this new one overcomes the unwanted effects while maintaining the demethylation efficiency. The authors demonstrate its application for ecological epigenetic experiments: testing transgenerational effects of plant–plant competition.
This novel method could be better suited for experimental studies seeking valuable insights into ecological epigenetics. As it’s based on periodical spraying of azacytidine on established plants, it’s suitable for clonal species reproducing asexually, and it opens the possibility of community-level experimental demethylation of plants.
Motion vision is an important source of information for many animals. It facilitates an animal’s movement through an environment, as well as being essential for locating prey and detecting predators. However, information on the conditions for motion vision in natural environments is limited.
To address this, Bian et al. have developed an innovative approach that combines novel field techniques with tools from 3D animation to determine how habitat structure, weather and motion vision influence animal behaviour. Their project focuses on Australia’s charismatic dragon lizards, and will place the animals’ motion displays in a visual-ecological context. The application of this approach goes well beyond this topic and the authors suggest the motion graphic technologies is a valuable tool for investigating the visual ecology of animals in a range of environments and at different spatial and temporal scales.
The seasonal long-distance migration of all kinds of animals – from whales to dragonflies to amphibians to birds – is as astonishing a feat as it is mysterious and this is an especially exciting time to study migratory animals. In the past 20 years, rapidly advancing technologies – from tracking devices, to stable isotopes in tissues, to genomics and analytical techniques for the analysis of ring re-encounter databases – mean that it’s now possible to follow many animals throughout the year and solve many of the mysteries of migration.
What is Migratory Connectivity?
One of the many important things we’re now able to measure is migratory connectivity, the connections of migratory individuals and populations between seasons. There are really two components of migratory connectivity:
Linking the geography of where individuals and populations occur between seasons.
The extent, or strength, of co-occurrence of individuals and populations between seasons.
More than anything else, the phenotype of an organism determines how it interacts with the environment. It’s subject to natural selection, and may help to unravel the underlying evolutionary processes. So shape traits are key elements in many ecological and biological studies.
Commonly, basic parameters like distances, areas, angles, or derived ratios are used to describe and compare the shapes of organisms. These parameters usually work well in organisms with a regular body plan. The shape of irregular organisms – such as many plants, fungi, sponges or corals – is mainly determined by environmental factors and often lacks the distinct landmarks needed for traditional morphometric methods. The application of these methods is problematic and shapes are more often categorised than actually measured.
As scientists though, we favour independent statistical analyses, and there’s an urgent need for reliable shape characterisation based on numerical approaches. So, scientists often determine complexity parameters such as surface/volume ratios, rugosity, or the level of branching. However, these parameters all share the same drawback: they are delineated to a univariate number, taking information from one or few spatial scales and because of this essential information is lost. Continue reading →
Many animals rely on movement to find prey and avoid predators. Movement is also an essential component of the territorial displays of lizards, comprising tail, limb, head and whole-body movements.
For the first time, digital animation has been used as a research tool to examine how the effectiveness of a lizard’s territorial display varies across ecological environments and conditions. The new research was published today in the journal Methods in Ecology and Evolution.
The BES Microbial Ecology Special Interest Group is running a workshop today (Thursday 2 November) on Novel Tools for Microbial Ecology. To compliment this workshop, Xavier Harrison has edited a Virtual Issue of the best Methods in Ecology and Evolution articles on advances in methods of studying microbial evolution and ecology from the past few years.
Advances in Next-Generation Sequencing (NGS) technology now allow us to study associations between hosts and their microbial communities in unprecedented detail. However, studies investigating host-microbe interactions in the field of ecology and evolution are dominated by 16S and ITS amplicon sequencing. While amplicon sequencing is a useful tool for describing microbial community composition, it is limited in its ability to quantify the function(s) performed by members of those communities. Characterising function is vital to understanding how microbes and their hosts interact, and consequently whether those interactions are adaptive for, or detrimental to, the host. The articles in this Virtual Issue cover a broad suite of approaches that allow us to study host-microbe and microbe-microbe interactions in novel ways.
How do we know how many fish there are in the ocean? 1000, 1 billion, 1000 billion? We can’t catch them all and count – that’s not practical. Nor can we make observations from Earth-orbiting satellites – light does not penetrate far into the ocean. What we can use is sound.
Sound travels well in water (faster and further than it does in air), so we can use scientific SONAR (echosounders) to produce sound waves and record backscatter from organisms and communities. This provides information concerning their biomass, distribution and behaviour. A recent study used echoes from the mesopelagic zone (200 – 1,000m) to predict global mesopelagic fish biomass to be between 11 and 15 billion tonnes (that’s a lot), suggesting that mesopelagic fish communities could potentially provide global food security.
10 mesopelagic classes are shown for the open-ocean, echo intensity (a proxy for biomass) increases from blue to red. Coastal zones excluded. Longhurst provinces overlaid. Shapefile here. Proud et al. (2017)
The comparative methods we use to study the evolution of traits are mainly based on the idea that since species share a common evolutionary history, the traits observed on these lineages will share this same history. In the light of phylogenetics, we can always make a good bet about how a species will look if we know how closely related it is to another species or group. Comparative models aim to quantify the likelihood of our bet being right and use the same principle to estimate how fast evolutionary changes accumulate over time. Continue reading →