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Workshop Morphometrics

  

Morphometrics Workshop in Naturalis museum
Tue 24 Sept. – Thu 26 Sept. 2013
Naturalis museum, Leiden

The workshop will combine introductory lectures on the different proposed topics, informal discussions, training sessions that include software demonstrations and practical examples on data, and talk on participant's studies.

Participation to the workshop is free of charge, and everybody is welcome to attend and join the discussion (students, PhD, researchers ...). A registration is asked in order to prepare the workshop as best as possible, and to meet the needs of scientists interested in morphometrics. Therefore, we ask you to send the registration form as soon as possible to thibaut.demeulemeester@naturalis.nl.  (download registration form)



Practical informations:
The workshop will be held in the Atelier, Pesthuis, Naturalis (Darwinweg 2).
>> go to all Practical information for more details.

Lecturers:
Andrea Cardini (University of Modena, Italy)
Vincent Debat (Museum National d'Histoire Naturelle, Paris)
- Menno Schilthuizen (Naturalis)
- Timo van der Niet (Naturalis)
- Adrien Perrard (Museum National d'Histoire Naturelle, Paris)
- Denis Michez (University of Mons, Belgium)
- Peter Schalk (ETI, Naturalis)
- Soraya Sierra (pro-iBiosphere, Naturalis)
- Willem Renema (Naturalis)


Program:
Program

In the framework of the workshop, we also invite you to these events that you will certainly enjoy:
  • Digiborrel of the FES Digitalization project, on the Wed 25th from 16:30: presentations on the project and on the digitalization of the collection,  and drinks! Click here for details.
  • Lecture of Prof. Alexander J. Werth (Hampden-Sydney College, USA) on biomechanics, entitled, "Becoming Jonah: Analyzing Forces and Flows in the Whale Mouth". On Thu 26th 16:00.

Tue 24, 9:30-12:00. Introduction to landmark-based image analysis. 

Lecturer: Andrea Cardini (University of Modena, Italy)

Abstract: Landmark-based image analysis (LIA) is a set of methods which belong to a larger family of techniques known as geometric morphometrics. The aim of LIA is to extract size and shape information from images to study how they vary and covary in biology. It represents the most modern form of morphometrics, a discipline with a century long history. LIA makes extensive use of the advances in computer technology and digital imaging to analyse and collect data within a rigorous statistical framework. Thanks to the combination of analytical power and intuitive visualizations using computer graphics, LIA has rapidly emerged as one of the most widely applied methods in biomedicine and it is central to the emerging field of phenomics, the comprehensive study of phenotypes.

Topics: Brief introduction to morphometrics and landmark based geometric morphometrics; Exploration of multivariate patterns of shape variation (PCA and cluster analysis); Group differences (permutation tests, discriminant analysis)

Area of interest: Researchers working on morphometrics in general, taxonomy, ecology, and functional morphology might be interested in this session


Tue 24, 13:00-15:00. Size effect in human sex: examples of shape analysis in human biology

Lecturer: Andrea Cardini (University of Modena, Italy)

Abstract: Using simple step by step examples, it will be shown how landmark-based image analysis (LIA) can provide intuitive but accurate numerical insight into aspects of human biology such as differences between craniofacial morphology of men and women: differences will be measured, tested, quantified in terms of magnitude, and visualized using shape diagrams.

Topics: Association between variables: multivariate regression (with examples from the study of allometry and/or geographic variation); 'size-correction' using a MANCOVA model, partial least square; introduction on advanced topics: comparative methods or semilandmarks.

Area of interest: Researchers working on morphometrics in general, taxonomy, ecology, and functional morphology might be interested in this session.

 

Tue 24, 15:30-17:00. Data acquisition

Lecturer: Willem Renema (Naturalis)

Abstract: We propose a session on data acquisition with particular interest on 3D morphometrics. The session includes a demonstration of the CT-scan for shape data acquisition.

Topics: Data acquisition; 3D Morphometrics; CT-scan.

Area of interest: Researchers working on morphometrics in general, taxonomy, ecology, and functional morphology might be interested in this session.

 

Wed 25, 9:00-10:00. Procrustean morphometrics and phylogeny

Lecturer: Andrea Cardini (University of Modena, Italy)

Abstract: Form and genes often tell different stories about the evolution of animals, with molecular data generally considered to be more objective than morphological data. However, form provides the basis for the description of organisms, and the study of fossils crucially depends on morphology. Complex organisms tend to evolve as ‘mosaics’, in which parts may be modified at varying rates and in response to different selective pressures. Thus, individual anatomical regions may contain different phylogenetic signals. Studies of the potential of different functional and developmental modules as proxies for phylogenetic divergence in modern lineages provide a framework that may help in modeling the morphological evolution of present and fossil species.

Topics: Phylogenetic signal in shape; selection pressure on forms; shape evolution.

Area of interest: Researchers working on evolutionary biology, and systematics might be interested in this session.

 

Wed 25, 10:00-15:00. Workshop shape and phylogeny

Abstract: Researchers are invited to informally present their own work and having a discussion about it. We invite them to show a few slides or even doing an analysis with the software and at the same time asking questions, discussing etc. The workshop on the study last for about 45 mins for both the presentation and discussion. This includes a presentation of ca 20 mins followed by an interactive discussion, questions (the audience asking the speaker but also the speaker asking the audience), comments, software demonstration etc.

Topics: Phylogenetic signal in shape; selection pressure on forms; shape evolution.

Communications: Adrien Perrard; Timo van der Niet

Area of interest: Researchers working on evolutionary biology, and systematics might be interested in this session.

 

Wed 25, 15:30-17:00. Short talks on morphometrics

Lecturer: Researchers and students

Abstract: Researchers are invited to present short talks (10-15min) on their works dedicated to the use of morphometric data.

Topics: Shape analyses.

Area of interest: Researchers working on morphometrics in general, taxonomy and systematics, ecology, functional morphology, and evolutionary biology might be interested in this session.

 

Thu 26, 9:00-10:30. Shape asymmetry

Lecturer: Vincent Debat (Museum National d'Histoire Naturelle, Paris)

Abstract: What are the sources of phenotypic variation and which factors shape this variation are fundamental questions of developmental and evolutionary biology. Despite this simple formulation and intense research, controversy remains. Three points are particularly discussed: (1) whether adaptive developmental mechanisms buffering variation exist at all; (2) if yes, do they involve specific genes and processes, i.e., different from those involved in the development of the traits that are buffered?; and (3) whether different mechanisms specifically buffer the various sources of variation, i.e., genetic, environmental and stochastic, or whether a generalist process buffers them all at once. We advocate that experimental work integrating different levels of analysis will improve our understanding of the origin of phenotypic variation and thus help answering these contentious questions.

Topics: Development of organisms; developmental stability; canalization; plasticity; fluctuating asymmetry; shape diversification; chirality.

Area of interest: Researchers working on evolutionary biology, developmental biology, and ecology might be interested in this session

 

Thu 26, 13:00-14:30eTaxonomy and taxa identification

Abstract: We propose a session on eTaxonomy, image recognition, automated identification tools, constructing morphological databases from marked-up literature, linking biodiversity data to collections/images/DNA/literature, a.o.. Following the lecture, researchers are invited to present talks on their works dedicated to this field. Or it can be a friendly discussion on the topic among reserachers attending the session.

Topics: image recognition and shape analyses; what morphometrics can bring to taxonomists; automated identification of taxa; e-tools and e-taxonomy; interoperability (linking data); automated digitalization of landmarks.

Communications: Thibaut De Meulemeester; Peter Schalk; Soraya Sierra; Rutger Vos; Sylvia Mota de Olivera; Jeremy Miller

Area of interest: Researchers working on morphometrics in general, taxonomy, ecology, and computer science might be interested in this session.

 

Thu 26, 15:00-16:30. Shape analyses of fossils

Abstract: We propose a session on the new insights in paleontology and what morphometrics can bring to paleontologists. Following a lecture, researchers are invited to present their works dedicated to the use of morphometric data in paleontology.

Topics: New insights in paleontology; what morphometrics can bring to paleontologists; missing landmarks; integrating fossils and extant specimens; calibration of phylogeny.

Area of interest: Researchers working on paleontology, taxonomy, systematics, ecology, and anthropology might be interested in this session.

 

List of Participants

Communications

Andrea Cardini: Introduction to landmark-based image analysis

Landmark-based image analysis (LIA) is a set of methods which belong to a larger family of techniques known as geometric morphometrics. The aim of LIA is to extract size and shape information from images to study how they vary and covary in biology. It represents the most modern form of morphometrics, a discipline with a century long history. LIA makes extensive use of the advances in computer technology and digital imaging to analyse and collect data within a rigorous statistical framework. Thanks to the combination of analytical power and intuitive visualizations using computer graphics, LIA has rapidly emerged as one of the most widely applied methods in biomedicine and it is central to the emerging field of phenomics, the comprehensive study of phenotypes.

Andrea Cardini: Size effect in human sex: examples of shape analysis in human biology

Using simple step by step examples, it will be shown how landmark-based image analysis (LIA) can provide intuitive but accurate numerical insight into aspects of human biology such as differences between craniofacial morphology of men and women: differences will be measured, tested, quantified in terms of magnitude, and visualized using shape diagrams.

Tara Chapman: Comparison of Neandertal bones with anatomically modern human bones using quadric surface fitting

Laura Cotton: Reticulate Nummulites through space and time: a work in progress

Ton De WinterIs GM applicable to coiled gastropod shells?

Vincent Debat: Is GM applicable to coiled gastropod shells?

Jozsef Gemltitle to be provided

Denis Michez: title to be provided

Jeremy Miller: title to be provided

Sylvia Mota de Oliveratitle to be provided

Thuong Nguyen PhucSkeletal deformities in gilthead sea bream (Sparus aurata): a multi-methodological approach

Katja Peijnenburg: Morpological divergence of marine lake populations**

Adrien Perrard: Evolution of the wing shape in social wasps: from the colony to the family. 

In order to understand the evolution of wing shape in social wasps, I studied the wing shape of hornets at different taxonomic scales: within a colony, between the population of a single species, between the species of the hornet genus and between the different genera of social wasps. As the shape variation may be driven by biological differences we tested the difference of wing shape of biological groups using cross-validated discriminant analyses and we found that the wing shape could discriminate surprisingly well genera, species, but also populations and castes within a species. To go further, we explored whether the wing shape variability could be explained by the evolutionary history of the different species. One method used to test for the congruence between the phylogenies and continuous character is the test of the phylogenetic signal. This test can be applied using different methods such as the permutation of the tips of a phylogenetic tree mapped within the morphospace. Each method has its advantages and disadvantages, but the phylomorphospace enable a more visual and detailed analysis of the evolution of the shape. This test tells us that the wing shape of social wasps is influenced by the evolutionary history of the species, but also by other factors. However, these analyses relies a lot on the phylogenetic trees used, but phylogenetic relationships are themselves inferences subject to uncertainty or errors. As wing shape is easily measured using already sampled collections, I will discuss the potential and limits of this marker for phylogenetic reconstructions.

Peter Schalktitle to be provided

Menno Schilthuizen: title to be provided

Soraya SierraConstructing morphological databases from marked-up literature & linking biodiversity data: the pro-iBiosphere approach

In the framework of the EU FP7 e-infrastructure pro-iBiosphere project (coordinated by Naturalis) various pilots are being conducted. Results on pilots addressing the re-use of morphological characters from published species descriptions and (ii) interoperability between taxon treatments from both legacy and prospective literature from three organismic domains (fungi, plants and animals) will be presented.

Timo van der Niet: title to be provided

Flora van Glabbeek: title to be provided

Myriam van Walsum: Geometric morphometrics in intra- and intercomparison of internal molar morphology in two hominin species

Preliminary research indicated that two species of hominin in South Africa around 2.5-2mya (Australopithecus africanus and Paranthropus robustus) could be well differentiated on basis of EDJ molar shape (enamel-dentine junction: where dentine and enamel meet, inside the molar). A specific trait (protostylid) was considered to be especially distinctive and further research was carried out. Geometric morphometrics was applied to capture size and shape of the EDJ, including dentine horns and molar cervix. Initially, the aim was to use GM to quantify protostylid expression. However, it was found that the protostylid is a feature without clear beginning and end, and ranges in expression from being absent to being tripartite. Due to lack of homologous landmarks it was impossible to use GM analysis on the protostylid. I would like to discuss the limitations of GM in such a case.

Isabel Van Waveren: Selecting on differential growth velocity

Rutger Vostitle to be provided

Alex Werth: Becoming Jonah: Analyzing Forces and Flows in the Whale Mouth


       

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