A new doctor on May 25 2012: Anna Runemark

As expected, Anna Runemark succesfully defended her excellent PhD-thesis on May 25 2012, and lab members and department colleagues celebrated this with a great party on the evening the same day. Below are some pictures from the party in the Ecology Building (thankyou to the photographer My Gustafsson who also has her own photoblog which you can visit here). 

Anna was understandably very happy after getting her lizard present from her co-advisor Bengt Hansson. 

Erik with the Faculty Opponent Prof. Scott V. Edwards (Harvard University)

It was great to have four out of my five previous PhD-students with me this memorable evening. Here with Fabrice Eroukhmanoff (left, currently in Norway) and the new doctor Anna Runemark (right). 

Jessica Abbott also seemed to have a good time... 

...as had hopefully also the other Jessica (Dr. Ware, from Rutgers University), who was a member of the thesis committé and was sitting close to Scott Edwards during the dinner. 

New postdoc Lesley Lancaster was probably a bit overwhelmed and still jetlagged from her recent arrival from the US. 

Our new book "The Adaptive Landscape in Evolutionary Biology" is now out!

Posted by Erik Svensson

Together with my colleague Ryan Calsbeek at Dartmouth College (USA), I am pleased to announce that our new edited volume "The Adaptive Landscape in Evolutionary Biology" (Published by Oxford University Press) is now out!

This volume marks the 80-year anniversary of late population geneticist Sewall Wright's first formulation of the Adaptive Landscape concept, which subsequently became so influential in population genetics, ecology and evolutionary biology. Both Ryan and I hope that this book will be of interest to both established researchers, postdocs and PhD-students.

We hope that graduate students will digest and discuss the contents of  chapters of this volume as part of reading groups, for instance. We have several prominent chapter contributors, and you can read more about them here.

You can order this book easily, either directly from Oxford,  or from Amazon.com. Order your copy today - before it is sold out!

Fusing theory and data: a plea for help from Dan Bolnick

Posted by Erik Svensson


I got a request from Andrew Hendry, who in turn got a request from Dan Bolnick (University of Texas, at Austin) about the relationship between theory and data. There is a blog post at the  blog by Andrew Hendry's lab entitled "Fusing theory and data: a plea for help from Dan Bolnick". You might want to read the blog post by Dan and provide your comments and suggestions here, as I have done. This is an excellent example of the kind of scientific discussions that we could (and should) have on blogs, rather than keeping them at local coffee rooms. So take the opportunity to provide input and be part of the global research campus!

When Biologists move to the dark side: working hand in hand with physicists to understand the role of color in the evolution of species

 PART 2

 *BY MAREN WELLENREUTHER, ANNA RUNEMARK AND MIKKEL BRYDEGAARD

 

Did you know that species can be measured as aerosols? Using lasers and dark field spectroscopy for remote classification of animals.

To improve the temporal and spatial resolution of insect movement, we started to think about novel ways to use species color information to track individual movement and interactions. At one of our meetings, the Physicists suggested to use LIDAR technologies and dark field spectroscopy to track the movement of individual damselflies as they had discovered that they could be treated just like large bio-aerosols. Laser radar or LIDAR stands for Light Detection And Ranging and is typically used to remotely measure the size distributions and composition of aerosols in the atmosphere. Recently, fluorescence LIDARs were developed  for the detection of biological aerosols in relation to bio-warfare such as anthrax, but they are slowly getting discovered by other scientists and are starting  to be applied outside this area. In this context, it should be noted that Radar technology is  of limited in insect detection because the small size of insects means that they are often too small to be detected by the Radar-wavelengths and hence no discrimination can be provided. , LIDARs, on the other hand, have the capability to capture fine scale temporal and spatial insect movements, as well as capture multiple color/polarisation details. Due to these characteristics, LIDARs can capture multiple movements in time and space and classify flying aerosol particles (e.g. insects) into discrete groups (e.g. species and sexes). We have shown these applications of LIDAR technologies in field feasibility studies here (Brydegaard, Guan et al. 2009), here (Guan, Brydegaard et al. 2010) and here (Brydegaard, Lundin et al. 2010).

Figure from (Runemark, Wellenreuther et al. 2012). Setup of the experiment. T: Newtonian telescope. C: Calibration site, B: Dark box termination. Light is collected by a 1mm UV fiber in the focal plane of the telescope and fed to a compact spectrometer. Distance from telescope to termination was 95 m of which the first 55 m cover grassland and the remaining 40 m cover the river Klingavälsån in Skåne, Sweden.

In addition to the use of LIDARs, it is also possible to use sunlight-based passive sensing methods to study flying insects. One passive sensing method, which is more economic and thus might be of interest to research groups with little funding, makes the use of sunlight and uses the back-scattering of animals (reflexes) that intersect the field of view. This method is called dark field spectroscopy (see e.g. http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=06134630). By analyzing the spectral signature (color) of the reflex, one can classify insects to species level and even separate sexes (if they differ in color). By applying this method, we could determine the sex of each damselfly individual that intersected the field of view, and this allowed us to study, for instance, sex specific activity patterns in relation to temperature and wind speed (Runemark, Wellenreuther et al. 2012). This setup also has the advantage of capturing interactions that occur at fast temporal scales, which, in contrast, are impossible to capture with the human eye. Just think of individual damselflies chasing each other above the river surface. In such a situation, where many damselflies belonging to different species and sexes interact in a dynamic interplay, the human eyes are not capable to capture the temporal and spatial resolution of such species interactions. The passive sensing setup, however, allowed us to study both pre-copula mating interactions between a male and female crossing the river (a female crosses the telescopes field of view approximately 0.1 seconds after a male) and males chasing after females (a male crosses the telescopes field of view approximately 1 second after a female).

Figure from (Runemark, Wellenreuther et al. 2012). Interactions between Calopteryx males and females. Note that there is a high blue peak just to the left of zero, indicating that it is quite common that males appear very shortly before females. This is most likely due to precopulas crossing the river. Approximately one second after a female has passed, there is a higher probability of a male passing too, probably males chasing the female. As expected this peak is less well-defined as the variation in distance is larger for chasing males than for precopulas.

Another interesting application of electro optical systems is the study of nocturnal migration in birds. Traditionally, nocturnal bird migration has been studied using RADARs, thermal cameras or moon watching. LIDAR systems, however, can significantly improve on those methods because LIDARs capture information about the color and plumage microstructure of migrating species. With this color information, it is then possible to classify some of the birds to the species level, as it is shown in the Figure below. 

Figures from (Brydegaard, Lundin et al. 2010) and (Lundin, Samuelsson et al. 2011). 

Lessons learned: What we as Biologists have learned from working with physicists

Color is of utmost importance in many animal systems, and it is therefore clear that many biologists wish to study and quantify color. The first step when doing so is to realize that this is not a trivial undertaking, and that we all need to first take a step back and carefully think about what we really want to do. Think of the photons as living beings, where are they born? Where do they go, what do they do and how do they change before their death when your detect them? What part of the animal do we want to study, what spatial and temporal resolution do we want, which animal is the receiver of the color signal and so on.  

Where from now? Future perspectives

Some of the applications described in this blog post have implications for the study of vector-borne diseases, the study of pollination, quantification of habitat availability for conservation issues, presence/absence of agricultural pests, and the study of predator prey interactions. We are collaborating with a Pan-African spectroscopy network, and in September, we will hold a workshop on realistic remote sensing methods for entomology. The aim is to remotely determine the flight direction, blood meal sizes and individual age of insects. We are looking for new biological questions that these spectroscopy groups, which are dispersed over 6 African countries, could address using setups that are similar to that described above (Runemark, Wellenreuther et al. 2012). We, therefore, greatly welcome comments and ideas in response to this blog post. The member countries are from east Kenya, Ghana, Burkina Faso, Mali, Ivory Coast and Senegal. If you wish to collaborate with any of the research groups, please contact Mikkel.Brydegaard@fysik.lth.se.

Some basic advice for biologists that would like to measure color

1. Read up on the vision system of your study species to make sure that the spectral domains you study are actually what they – or for instance their predators use. This might mean that you need to adjust your measuring setup to the question posed (e.g. if you study sexually selected traits the vision system of the study species is of interest, whereas that of the predator is more relevant if you want to study crypsis).
2. Standardize the setup, including the light environment whenever possible. It is also whortwhile to spend  a little time on making a standardized photobox because this will save you time in the long-run, when it comes to the evaluation of your data. In addition, using standardized setups ensures that you obtain more accurate data.
3. When standardized illumination cannot be used, use a ColorChecker reference board to characterize the spectral bands of your imaging system for the given situation.
4. When correcting for the spectral flatness and the illumination profile, you should get diffuse reflectances between zero and one.
5. To measure ‘color’ of background environments, measurements that are taken over an entire day cycle are ideal. If that is not possible to achieve, try to take your measurements at the same time of the day, facing the same cardinal direction. Considering the radiative transport in the atmosphere, vegetation, canopies and water environment are complex issues that the remote sensing community has had to deal with for decades. In fact, there are even journals  that are dedicated to this particular topic.
6. Use polarization filters in front of the flash and objective to avoid specular reflexes – the shiny white reflex on, for instance, a tomato. These reflexes do not  contain any valid information about the color of the tomato, and we need to, therefore, avoid them. This principle is, however, not applicable to species which have structural colors, such as the Calopteryx damselfly species that we study. For an example of how color can be quantified for such animals, see (Brydegaard, Guan et al. 2009).
7. If the character studied is represented in a biologically relevant way by the RGB bands in e.g. commercially available cameras, the best way to make use of the information is to use the information given in each pixel. This provides information on, for instance, the variance in addition to the mean, see (Brydegaard, Runemark et al. 2012) for an example.
8. Be aware that a large number of commercially available multispectral and hyper spectral imagers are capable of capturing continuous spectra in every pixel, or images at all wavelength visible to your study species. Systems with a few spectral bands can easily be built at home using cameras and filters wheels of the shelf.
9.  It is important to take color vision into account when designing experiments. It is of limited use with, for instance, mate choice trials in glass or plastics boxes for a species with a sexually selected ornament in the UV domain, as glass and plastic might filter out the relevant part of the UV spectrum.
10. Don’t be afraid to knock on the door of the Physics department at your facility, they might just have the equipment you are looking for. Starting a communication process with physicists can help with your ideas and experiments, but this communication can also help the physicists to think about new problems that are biologically relevant. The problems that biologists face when studying the natural world the are seldom trivial and the challenge that these questions bring to a physicist might be both stimulating and entertaining from a Physics and engineering perspective.

 References

Brydegaard, M., Z. Guan, et al. (2009). "Fluorescence LIDAR imaging of insects - a feasibility study." Applied Optics 48(30): 5642-5888.

Brydegaard, M., P. Lundin, et al. (2010). "Feasibility study: fluorescence lidar for remote bird classification." Appl. Opt. 49(24): 4531-4544.

Brydegaard, M., A. Runemark, et al. (2012). "Chemometric approach to chromatic spatial variance. Case study: patchiness of the Skyros wall lizard." Journal of Chemometrics: n/a-n/a.

Guan, Z., M. Brydegaard, et al. (2010). "Insect monitoring with fluorescence lidar techniques: field experiments." Appl. Opt. 49(27): 5133-5142.

Lundin, P., P. Samuelsson, et al. (2011). "Remote nocturnal bird classification by spectroscopy in extended wavelength ranges." Appl. Opt. 50(20): 3396-3411.

Runemark, A., M. Wellenreuther, et al. (2012). "Rare Events in Remote Dark Field Spectroscopy: An Ecological Case study of Insects." Journal of Selected Topics in Quantum Electronics, IEEE PP(99): 1-1.

Minisymposium May 24 2012: "Biogeography and Evolution"

We are happy to announce an exciting Minisymposium entitled "Biogeography and Evolution" on May 24 2012 that will take place on the afternoon the day preceeding Anna Runemarks PhD-thesis defence (May 25). We have four excellent speakers that will present some exciting talks this afternoon. This symposium is open for everyone, whether from the Biology Department of from elsewhere. Full details of the programme and the titles of the talks are presented below:

Minisymposium on Biogeography and 

Evolution

                 

May 24, 13.00 - 16.00                               

"Blue Hall", Ecology Building, Department of Biology, Lund

13.00-13.40 Scott V. Edwards (Harvard University, USA)  “The phylogeography-phylogenetics continuum: a look to the future”

13.50-14.20 Jessica Ware (Rutgers University, USA) "Here be dragons: biodgeography and age of Petaluridae, the petaltail dragonflies"

14.30-14.50 Coffee

14.50 - 15.20 Alexandre Antonelli (Gothenburg University, Sweden) "Ecology meets Biogeography: A Multi-Disciplinary Approach to Study Neotropical Diversification"

15.30- 15.50 Folmer Bokma (Umeå University, Sweden) ”Why species may not adapt”

15.50 - 16.00 Discussion and concluding remarks

Symposium open for all interested. No registration required.

Welcome!


Bengt Hansson, Anna Runemark & Erik Svensson

On sexual selection, non-ecological speciation and species coexistence

Next week's lab-meeting will focus on a topic that is closely connected to our coming ESF-funded workshop in August 2012 about non-ecological and non-adaptive speciation: The problem how weakly ecologically differentiated species might still coexist, in spite of being formed by sexual selection and when there are no or weak niche differences in between them. A recent paper in Nature presents a new model that aims to solve this problem (Abstract, link and authors posted below). You can download this paper here.

Time and place of lab-meeting as usual: "Argumentet" at 13.30, Wednesday May 16.

Sexual selection enables long-term coexistence despite ecological equivalence

• Leithen K. M’Gonigle,
• Rupert Mazzucco,
• Sarah P. Otto
• & Ulf Dieckmann

• Affiliations
• Contributions
• Corresponding author

Nature

 

484,

 

506–509

 

(26 April 2012)

 

doi:10.1038/nature10971

Received

 

09 August 2011 

Accepted

 

17 February 2012 

Published online

 

01 April 2012

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Empirical data indicate that sexual preferences are critical for maintaining species boundaries^{1, 2, 3, 4}, yet theoretical work has suggested that, on their own, they can have only a minimal role in maintaining biodiversity^{5, 6, 7, 8, 9}. This is because long-term coexistence within overlapping ranges is thought to be unlikely in the absence of ecological differentiation⁹. Here we challenge this widely held view by generalizing a standard model of sexual selection to include two ubiquitous features of populations with sexual selection: spatial variation in local carrying capacity, and mate-search costs in females. We show that, when these two features are combined, sexual preferences can single-handedly maintain coexistence, even when spatial variation in local carrying capacity is so slight that it might go unnoticed empirically. This theoretical study demonstrates that sexual selection alone can promote the long-term coexistence of ecologically equivalent species with overlapping ranges, and it thus provides a novel explanation for the maintenance of species diversity.

New PhD-thesis from the lab: Anna Runemark and evolution on islands

Posted by Erik Svensson

Some of the proudest moments in the careers and life of advisors come when their students successfully finish their PhD-theses. Now it is time again, this time for Anna Runemark, who will defend her PhD-thesis on Friday May 25 in the "Blue Hall" (Ecology Building, Department of Biology) at 09.30. The thesis defence is open to all interested, as with all PhD-thesis defences at our university.

The Science Faculty's external opponent is Professor Scott Edwards from Harvard University. The examination committé consists of Drs. Alexandre Antonelli (Gothenburg University, Sweden), Folmer Bokma (Umeå University, Sweden) and Jessica Ware (Rutgers University, USA). On May 24 (Thursday, the day before Anna's thesis defence), we will have a small and informal research symposium with the opponent and the members of the thesis-committé entitled "Island Biology and Evolution", which will start at 13.00 in the "Blue Hall" (Ecology Building).

The title of the thesis is "Island biogeography and population divergence in the Skyros wall lizard". You can find a Swedish summary of the thesis here, and here is the link to the entire thesis, for those of you work at Lund University.

On a more personal note, Anna Runemark is my fifth PhD-student, preceeded by Jessica Abbott (2006), Thomas Gosden (2008), Fabrice Eroukhmanoff (2009) and Kristina ("Tina") Karlsson-Green (2010). I am proud of all these students, and I have learnt tremendously much from being an advisor of these five PhD-theses. Above all, I have learnt that there is not one way of being a good advisor or a good student - but many. 

There is thus no single "magic formula" to do an excellent PhD-thesis, but many different avenues. In a way, one could compare the writing of a thesis with the hill-climbing process on Sewall Wright's Adaptive Landscape: there are multiple adaptive peaks (excellent theses) and many different combinations of skills that make a good thesis. There are also many different kinds of students, each with different social and intellectual backgrounds, personalities, skills and interests. 

Equally, there are many different ways of a being a good advisor, and being a good advisor or a good student is, in itself, no guarantee for success. It is rather the combination of advisor and student that is crucial. One could perhaps compare this with the concept of genetic compatability in sexual selection: some combinations are less fit than others, even if the component parts (genes, advisors, students) do not differ and are excellent in isolation. 


The ideal student-advisor relationship is one of complementarity and mutual respect for each other's skills: The advisor provides the broader overview, theoretical and conceptual background and helps the student to see "the Big Picture" of the work, and forces the student to keep looking at the horizon, rather than dwelling in to methodological details. The student, on the other hand, should develop his/her methodological and technical skills and become "good" at it, and work to build his/her understanding of scientific concepts and how the thesis work can contribute to increased understanding of the natural world. I feel that Anna's thesis about a classical topic in evolutionary biology (evolution on islands) exemplifies this type of advisor-student collaboration that characterizes an excellent PhD-thesis.   

When Biologists move to the dark side: working hand in hand with physicists to understand the role of color in the evolution of species

PART 1 

 *by Maren Wellenreuther, Anna Runemark and Mikkel Brydegaard

We study a variety of species in our lab, such as ecotypes of isopods and color morphs of lizards and damselflies. In our work on these species, color is one of the main traits that we examine. This is because color affects crypsis (isopods), sexual selection and other life history traits (lizards and damselflies). However, examining color is not a trivial undertaking. For example, biologists often fail to account for differences in animal visual systems when modeling how species are perceived by con- and heterospecifics. Many also fail to realize that most cameras are not sufficiently spectrally resolved (they have 3 bands only) to capture color and that most spectrophotometers are not sufficiently spatially resolved to capture heterogeneity in color patterns (since they give averages rather than spatially resolved measures, consequently, both a donkey and a zebra would appear grey to a high resolution spectrometer). 

Ecotypes of isopods Asellus aquaticus, color morphs of the Skyros Wall Lizard Podarcis gaigeae, and different colors a mating couple of the structurally colored Calopteryx virgo. 

The beginnings…                      

When we first started to measure color, we realized how difficult this task actually is. This is particular true when one wants to conduct color experiments in natural or laboratory settings. What light sources are needed? What color vision does the color-signal-receiver have? Faced with these problems, we quickly recognized that we needed to communicate with people that know how to measure color. The Atomic Physics Section at Lund University has a group (Applied molecular spectroscopy and remote sensing) under the supervion of Sune Svanberg that, among other things, specializes in the measurement of color. First contact with the group was established in 2007 when Fabrice Eroukhmanoff was hoping to quantify the color of isopod ecotypes, of which one ecotype typically inhabits the reed habitat, while the other one prefers chara habitat. Fabrice wanted to quantify the color of different ecotypes. After talking to Mikkel Brydegaard Sørensen, a PhD student in Sune’s group, they realized that in order to compare the photographs, he needed to standardize them posteriori to account for different light environments. The color analyses are presented in, for example, here.  Discussions and exchange of ideas between our group and Sune’s group helped in the years to come to set up carefully planned experiments to examine color traits. 

To illustrate the point…measuring complex color traits in the Skyros Wall lizard

For Anna Runemark, who is studying color morphs of the Skyros Wall lizard but also dorsal coloration, color is one of the core traits of her studies. In her work, she is interested in the strength and direction of sexual selection on different color morphs in island and mainland populations (see here). To measure color differences, Mikkel designed an optically isolated ‘photo-box’ with a standardized light environment (e.g. the only illumination source is the flash) and polarizing filters in front of the flash and the objective to avoid specular reflectance. As the distances from the flash vary with position in the box, the white background is used to interpolate an illumination profile on the lizard, and this was used to correct for illumination differences across the photograph. Lastly, to estimate the entire color probability distribution (includes information about both mean, variance, skewness, kurtosis etc., see e.g. the 2D examples in the figure below), the color of each pixel of the measured colour patch was quantified, spatially accumulated and then divided by the number of pixels to obtain the probability. This method is presented in a paper found here

Figure 4-taken from (Brydegaard, Runemark et al. 2012). Upper row: reflectance distributions for a homogeneously colored yellow-throated lizard. Lower row: corresponding distributions for a orange-yellow patchy specimen. Left column: three 1D distributions for each spectral band. Middle column: 2D chromatic plane distributions color coded with corresponding colors for the two example specimen. Right column: iso-surfaces encapsulating probabilities higher than 1% in the 3D RGB color space of the two sample specimens. Surfaces are coded with corresponding colors.

After these initial dialogs between biologists and physicist, it became clear that we can both learn from each other. We as biologists have an interest in capturing color traits of animals accurately and precisely, while physicist that study natural phenomena have a need to understand the biological underpinnings. As a result of this initial integrative work, the Lund CAnMove group organized a symposium entitled ”The Biology-Physics Interface”. During this day, many of us met and presented our research and discussed ideas. 

Caption: CAnMove symposium ”The Biology-Physics Interface”. Sune Svanberg at the top, and Erik Svensson below.

References

Brydegaard, M., A. Runemark, et al. (2012). "Chemometric approach to chromatic spatial variance. Case study: patchiness of the Skyros wall lizard." Journal of Chemometrics

Eroukhmanoff, F., A. Hargeby, et al. (2009). "Parallelism and historical contingency during rapid ecotype divergence in an isopod." Journal of Evolutionary Biology 22(5): 1098-1110.

Runemark, A. and E. I. Svensson (2012). "Sexual selection as a promoter of population divergence in male phenotypic characters: a study on mainland and islet lizard populations." Biological Journal of the Linnean Society 106(2): 374-389.