Monthly Archives: November 2015

Molluscs in the news

Two news items came to my attention today. The first has been taken from the Conch-L list and is about conservation of Florida land snails. “Florida Fish and Wildlife [Conservation Commission] has just sent out a posting regarding endangered and threatened species. There are two proposed rulings on Tree snails. The one  is Liguus and the other is Orthalicus. Here is the Liguus and other species  link. http://myfwc.com/wildlifehabitats/imperiled/species-action-plans/”. Only Liguus fasciatus is mentioned, together with more than 50 species of other phyla.

Liguus Florida

The ‘Science in the news’ site had an item on natural history museums and how these institutions, behind the scenes, are centers of cutting-edge research. One example is the recent discovery of a Plekocheilus species, collected back in the 1800s. More brushing off the dust than cutting the edge, but anyway…

Photo of the day (163): Drymaeus and Cerion

François van der Hoeven regularly sends reports of small expeditions to discover forgotten and new things on the island of Curaçao. This time a report on their wanderings at plantation Wacao. At the end of their trip the rain started pouring. Time for snails to become awake and be on the move…

29 Nu gaan de slakken lopen - foto Carel 30 Zelfs de Cerion uva - foto Carel

These two pictures of Drymaeus elongatus respectively Cerion uva were made by Carel de Haseth.

New paper published

A new paper was just published which may be of interest to collection managers and people with biohistorical interest. It is about the collection of ‘autographs’ in the Dautzenberg archives in the Royal Belgian Institute of Natural Sciences in Brussels, and contains letters or postcards of more than 450 persons contemporary to Dautzenberg (1849-1935). Of these handwritten correspondence nearly 70 examples are given, while the appendix has a full list of correspondents. For several of them new or additional biographical data are presented.

FC33

The paper can be freely downloaded following the link on my publications page.

Chilean bulimulids

Just published in a not-so-common journal for a taxonomical paper: Juan Francisco Araya’s new paper on Bulimulidae from the Atacama region in Chile. This desert-like environment is only seemingly unfavorable for snails and is little researched so far.

ArayaT1

The abstract reads: “The bulimulid genus Bostryx Troschel, 1847 is the most species-rich genus of land snails found in Chile, with the majority of its species found only in the northern part of the country, usually in arid coastal zones. This genus has been sparsely studied in Chile and there is little information on their distribution, diversity or ecology. Here, for the first time, a formal analysis of the diversity of bulimulids in the Region de Atacama, northern Chile, is reported. Of the seventeen species recorded for the area, most of themwere efectively found in the field collections and one record was based on literature. Five taxa are described as new: Bostryx ancavilorum sp. nov., Bostryx breurei sp. nov., Bostryx calderaensis sp. nov., Bostryx ireneae sp. nov. and Bostryx valdovinosi sp. nov., and the known geographic distribution of seven species is extended. Results reveal that the Region de Atacama is the richest region in terrestrial snails in Chile, after the Juan Fernandez Archipelago. All of the terrestrial molluscan species occurring in the area are endemic to Chile, most of them with restricted geographic distributions along the coastal zones, and none of them are currently protected by law. Further sampling in northern Chile will probably reveal more snail species to be discovered and described”. The study of Araya is thus a welcome additional to our knowledge of the Neotropical malacofauna.

Reference:
Araya, J.F. (2015). The Bulimulidae (Mollusca: Pulmonata) from the Region de Atacama, northern Chile. – PeerJ 3: e1383. Available at https://peerj.com/articles/1383.pdf

Copulation in Cuban Jeanneretia

The biology of Neotropical land snails is largely unknown, and data on copulation is only hard to find. Recently a study on the mating behaviour of some Jeanneretia in Cuba was done, which received the Unitas Malacologica Student Research Award 2014 (Hernández Quinta, 2015).

Hernandezf4

Major findings of the study are the variability in the location of the accessory copulation organ between different taxa, and the absence of a sensitive zone as observed in Polymita. The total duration of courtship appears to be relatively short compared to data from literature. A brief version of the study just appeared in the UM Newsletter.

Reference:
Hernández Quinta, M. (2015) Mating behaviour in Jeanneretia ss. (Helicoidea: Cepolidae), endemic of the western region of Cuba. – Unitas Malacologica Newsletter 35: 7-9.

New journal

It is not an every day activity, but recently the publishers Taylor & Francis (known from the Journal of Molluscan Studies) launched a new journal: Neotropical Biodiversity. It is an open access journal, but remarkable is it charges no author fees (the only other example I know is the European Journal of Taxonomy). The expenses of open access publishing in Neotropical Biodiversity are covered by Ecuador´s National Secretariat for Higher Education, Science, Technology and Innovation. This means there are no article publishing charges and your article will be freely available for everyone on publication.

TNEO

I was quite surprised about the involvement of the Ecuadorian government, but if this is a sign of real commitment with biodiversity research (and nature conservation) it is only to be appreciated very much. The scope of the journal is broad and the editorial board is dominated by Ecuadorians and Americans. The first issue is in progress and has so far papers on mites and frogs.

A welcome addition as outlet for papers on the Neotropics. Let’s hope that it will stimulate researchers in this realm to do research that is worth publishing in this journal.

 

3 days of 3D – Day 3

Wednesday 4-11-2015 Geometric Morphometrics (Microscribe and laser scanning)

3D Trex

10.30 – 11.00 Measuring shape in biology – a short guide to Geometric Morphometrics
Thibaut De Meulemeester – Naturalis Biodiversity Center

The basics of GMM will be introduced and explained with some examples using 2D and 3D morphometrics. Traditional morphometrics (distances, angles, ratios) is limited by influence of size, and the shape cannot be analyzed. There is GMM for, either with landmarks or outlines. Procures superimposition removes the non-shape variation (scale, translation, rotation). More information on http://www.transmittingscience.org/hystrix-yellow-book.

11.00 – 11.20 Tracking and printing dinosaurs: 3D scanning and 3D printing in the upcoming dinosaur exhibits in Naturalis
Anne Schulp – Naturalis Biodiversity Center

Next year, Naturalis will present a new Tyrannosaurus rex specimen, and in 2018, the new dinosaur gallery in the new museum will open. The developments in 3D imaging and 3D printing techniques have many applications in paleontology; not only in research but also in outreach and museology. The upcoming “Welcome T. rex”-exhibition at Naturalis will feature (the results of) 3D Laser scanning, 3D photogrammetry, CT-scanning and 3D printing. This short presentation will provide an overview of the ongoing 3D projects on and around the Naturalis T. rex.

11.20 – 11.50
Hans Cornelisse – GOM/Optical Measuring Techniques

Examples and possibilities using laser and light scanners. It can only be applied to non-live materials and ‘sees’ what humans see (not looking around the corner). Software to make your model visible is the crucial step.

11.50 – 12.20 “Why do different birds have different beaks? Linking shape with biomechanics”
Jen Bright – University of Sheffield

During evolution we see how animals change in shape to become better adapted to their environments, but what is not always clear is why a certain shape is better than another. Finite Element Analysis (FEA) is a method borrowed from engineering that can be used to see how complex shapes (like skulls and other bones) respond to forces that an animal encounters every day, like biting on food, running, or fighting. By using FEA together with shape analysis like geometric morphometrics, we can investigate how the relationship between shape and function works. Jen will show these ideas using examples from modern birds, and also show how everyone who is interested can help us build the biggest shape database of bird beaks ever collected!

Wrapping up

Especially the last lecture showed me that ‘borrowing’ a technique from a different discipline can further the progress in a research field. The application in the Mark my Bird project (markmybird.org) opens up the perspective to get a deep understanding of bird evolution once understanding functional morphology has progressed.

3 days of 3D – Day 2

Tuesday 3-11-2015 3D visualization

10.30 – 10.50 Photogrammetry, a poor man’s guide to 3D digitization
Edwin van Spronsen – Naturalis Biodiversity Center

Photogrammetry is a technique for turning photographs into 3D objects. All it requires is a digital camera and a computer to do the calculations. Agisoft software (free for 30 days). Typically, 10-100 photographs are needed from different angles. An additional bonus of photogrammetry – as compared to other 3D digitization techniques – is the fact that the original images will also provide a photorealistic texture of the object. It is a cheap, accurate and robust technique that produces highly realistic models for 3D printing, gaming and display on the web. Several collection objects from the museum have been digitized this way. Examples will be shown and do’s and don’ts will be discussed. So it is important to have the object totally in focus; use a stacking program (e.g., Helicon Stacking) to ensure this. Presentation can be made with ThreeJS, Adobe Acrobat, or dedicated viewers (Meshlab).

10.50 – 11.10 Visualizing shark jaws
Pepijn Kamminga (Mimics) – Naturalis Biodiversity Center

For his PhD research on the ecomorphology of the lower jaw in extant sharks, Pepijn Kamminga CT scanned a large part of the Naturalis’ shark spirit collection. The raw data produced from this method needs to be processed in order to be useable for quantitative analysis. In this presentation Pepijn focusses on the process of visualisation of shark jaws in 3D using the software package MIMICS. It is a relatively user-friendly program, which I also used myself, that allows segmentation of particular organs. Landmarking was done using Landmark Editor and MorphoJ (tomorrow more).

11.10 – 11.30 Visualizing the nothing: A reconstruction of the fossil fish brain
Sophie van der Hart – Naturalis Biodiversity Center & Institute of Biology, Leiden University

Fossils can provide important information about brain architecture by examining the openings and canals left in the brain. Traditionally, Xrays are used to visualize mineralised tissues like the skeleton. However, soft-tissue structures are usually poorly preserved or entirely missing in vertebrate fossils. This makes it extremely difficult to separate and follow the course of each individual nerve or fibre through the brain. Using three dimensional software for model reconstruction, a 3D model of the internal structure of the braincase can be achieved. Sophie will show that this virtual approach gives a reliable data base for studies in comparative anatomy and enables us to learn more about the evolution of the vertebrate brain.

11.30 – 12.00 Amira|Avizo: software solutions for 3D visualization and analysis
FEI: Amira/Avizo

Amira and Avizo are comprehensive, integrated software solutions for spatial data visualization, image processing, analysis and quantification dedicated respectively to life and materials sciences. The broad range of functionalities, exposed through an intuitive visual programming interface, enable the processing of extremely diverse kinds of images and data from any type of imaging device. This presentation will propose an overview of the software functionalities, highlighting the main features of the software with illustrations in paleontology, biology and materials science domains. FEI will in particular highlight a recently added feature dedicated to the robust detection and centerline tracing of fibers.

12.00 – 12.30 Blending in! Visualisation, animation and analysis of palaeontological data with Blender
Stephan Lautenschlager – University of Bristol

In the last decade, computer-aided visualisation and digital analysis techniques have revolutionised palaeontological research and transformed the way fossils can be studied. Computational methods, such as various forms of computed tomography (CT), finite element analysis (FEA) or multibody dynamics analysis (MDA), now provide a wealth of digital data with a potential to be used for research publications, conference contributions and public outreach activities. The freely available digital visualisation and modelling software Blender offers a powerful tool to visualise three-dimensional models and analytical data and to create animations. However, Blender holds further potential to perform different analyses by using the in-built Python interpreter. Two examples will be presented of how Blender can be used to analyse muscle function in theropod dinosaurs, such as Tyrannosaurus rex, and to study the locomotion of ichthyosaurs, a group of fossil marine reptiles. The initial learning curve is, however, very steep.

 Wrapping up

Some of the visualization programs are freeware, others (Avizo, Mimics) are very costly. Also there is much difference in ‘intuitively’ of the software packages. And although the end result is always eye-catching, the time investment can be cumbersome.

 

 

3 days of 3D – Day 1

The introduction of a new microCT scanner at Naturalis has lead to a series of presentations in the LiveScience hall. The programme is focussed mainly on vertebrates and plants, but as I have been doing some experiments with snails, I mention the event here.

Monday 2-11-2015 X-ray scanning

 

10.30 – 10.45
Introduction 3 days of 3D

10.45 – 11.05 Imaging shark jaws using Medical CT scanning
Pepijn Kaminga  – Naturalis Biodiversity Center

Jaws are essential in capturing and processing prey and should therefore be optimized by natural selection for this role. Consequently, jaw morphology is thought to reflect feeding habits, and is frequently used in ecomorphological and paleontological studies to explore the evolution of trophic diversity. However, it may not be a good predictor of feeding habits and the associations are often functionally inferred. To test the association between jaw diversity, diet and phylogeny, I studied jaw shape disparity together with detailed data on diet based on a literature survey in a phylogenetic context. I created three-dimensional (3D) reconstructions from computed tomography scans of 148 left lower jaws from 89 extant shark species. In this presentation I’ll elaborate on CT scanning and how a large part of the sharks from the Naturalis’ spirit collection is used for this purpose.

11.05 – 11.25 3D-imaging of flowers and pitchers
Barbara Gravendeel, Anita Dirks & Rachel Schwallier  – Naturalis Biodiversity Center & Institute of Biology, Leiden University

Background: Over the past 100 million years, orchid flowers became highly adapted to their pollinators and pitcher plants growing on nutrient poor soils evolved special leaf tip traps to obtain extra nutrients.

Goal: Obtain more insight in the evolutionary origin of the morphological adaptations of these plant groups.

Methods: Analysis of 3D scans made by Xradia tomography and the Sense handscanner.

Results: Vascular bundles visualized in 3D scans of orchid flowers support the hypothesis that stelidia evolved from stamens to ensure reproductive isolation. Leaf tip traps of pitcher plants evolved into shapes especially adapted to either catching insects or plant debris but not both.

11.25 – 11.45 Vision impossible? Shedding synchrotron light into deep-time evolution of the vertebrate skeleton
Martin Rücklin  – Naturalis Biodiversity Center

To visualize minute structures and minimal contrasts inside of fossils traditional CT or microCT technology reaches a limit. In order to overcome this problem the use of synchrotron tomography allows high energy, brilliance and enhanced contrasts inside of fossils. Using this method cell spaces and lines of arrested growth demonstrating growth inside of the skeleton are possible. In the talk I will demonstrate the possibility to reconstruct the development of the vertebrate skeleton in the first jawed vertebrates and future possibilities using developmental palaeobiology.

11.45 – 12.20 MicroCT scanning at Naturalis
Rob Langelaan and Bertie Joan van Heuven – Naturalis Biodiversity Center

X-ray scanning facilities at Naturalis, an introduction to our SkyScan and brand new Zeiss Xradia versa. In a live stream from the X-ray lab we will show how to set-up a scan, explain the possibilities of the new machine, which is one of the best lab-based MicroCT scanners available today and what we plan to do with it in the future.

Wrapping up

The different techniques that were shown each have there (dis)advantages and one need to carefully frame the research question and select the technique appropriate to the subject involved. Staining techniques may be needed, and one should keep in mind that – although these techniques are generally considered non-invasive – they can have an impact on the (museum) specimen.

Summarizing, these (partially) new techniques have hitherto been hardly used in malacology and it’s an interesting frontier of science. Curious to see how this will further develop.