Happy New 2013!

Posted by Erik Svensson

The year 2012 is now behind us, and we are looking forward to 2013. The past year was, I dare to say, extremely successful in terms of grant applications, good publications, events and activities. To mention just a few things: three new postdocs joined the lab (Yuma, Lesley, Natsu), one PhD-student defended her thesis in May (Anna Runemark), one postdoc got a "Junior Project Grant" from the Swedish Research Council (Maren) and Jessica got a large grant from the Crafoord Foundation, that has made it possible for her to recruit a new PhD-student to work on the flatworm experimental evolution project. I myself, got a large grant from The Swedish Research Council too, which I am of course very happy for. I certainly hope that 2013 will be as successful, for all of us, as was 2012. Well done, all of you!

Among publications, I could mention some nice papers in Ecology, Molecular Ecology and Trends in Ecology & Evolution, but there are certainly more. I was also happy to get my new volume "The Adaptive Landscape in Evolutionary Biology" out at Oxford University Press (co-edited with Ryan Calsbeek from Dartmouth College, USA). 

Below are some pictures from the past year. Keep up the good work, friends!

In December, postdoc Lesley Lancaster visited Erik in Dalby to run some generalized linear models in "R" to investigate the role of temperature on mating conflicts in the polymorphic damselfly Ischnura elegans. 

Earlier in December, lab members from EXEB and other colleagues at the Evolutionary Ecology Unit went for our annual Christmas Meeting. Here John, Jasmine and Anna Nordén enjoy the Christmas Table in the evening after the talks. 

And here are Jessica and Yuma in the same evening.

In January and February, Erik went to South Africa for field work with odonates in the Western Cape Province with Master's student Anna Nordén (right) and undergraduate Johanna Eklund (left). Here they both enjoy some of the wine of the Stellenbosch district. 

The arrival of our two Japanese postdocs Yuma and Natsu in May enabled us to start up some new projects, including one on Wing Interference Patterns (WIP:s) in Drosophila melanogaster and their role in mate choice and sexual selection. Here we see Yuma, Natsu, Jessica and Jostein Kjarandsen in the lab, doing mate choice trials (Erik is behind the camera). 

Anna Runemark receives postdoctoral research grant from the Swedish Research Council

It is with great pleasure and happiness that we note that Anna Runemark, who defended her PhD-student in May earlier this year, has received a prestiguous postdoctoral grant from The Swedish Research Council (VR). Congratulations Anna! This requires celebration with some sparkling wine at tomorrow's lab-meeting (December 11 at 10.30). The new postdoctoral grant system means that Anna will be employed at the Biology Department in Lund, being part of our lab, but will work abroad at the University of Oslo (Norway) for two of the coming three years. She will then perform research on the genomic consequences of homoploid hybridization among Passer-sparrows in southern Europe. 

Anna's achievement is well-deserved and impressive, particularly in the light of the severe competition for such grants (23 % success rate). To my knowledge, Anna was the only evolutionary biologist this year who got such a postdoc among the natural sciences in Sweden. Anna's achievement is hers, and hers only, but as a former PhD-advisor I do of course take some pride too, and takes the opportunity to boost my already big ego a bit further. I am glad that Anna keeps up my good statistics in terms of former PhD-students who get VR-postdocs: She is number five, out of five in total, resulting in a 100 % success rate (future students in this lab should take it as an encouragement and not feel stressed about it, I hope). 

We also have several other reasons to celebrate tomorrow: our postdoc Maren Wellenreuther got a "Junior Researcher" grant from VR earlier in November this year, and I myself also got a four-year grant from the same agency. Further, Jessica Abbott recently got 380 000 SEK for  buying equipment to the fly lab, and Maren got 100 000 SEK from the "Nilsson-Ehle Foundation". All in all a very successful year for the lab members in terms o grants, and hopefully this will continue in the near future. 

These are achievements we all should be proud of, whether we actually got a grant or not ourselves, as research is a collective enterprise and scientists do not work in isolation. One colleague's success can largely be attributed to his/her colleagues too, who have contributed to create an intellectually and scientifically stimulating research environment, and this is true whether you are a PhD-advisor, professor, lecturer, postdoc, PhD- or Master's student. 

Congratulations to Maren Wellenreuther for obtaining "Junior Project Grant"

The Swedish Research Council (VR) recently announced its grants decision for 2012, and I am happy to congratulate one of our lab-members and current postdoc Maren Wellenreuther, to have obtained a "Junior Project Grant" for the next four years. These highly attractive but competitive grants is one way of entering the job market and path towards a research or faculty position in Sweden. Competition was severe this year, as previous years, with only about 16 % of all applications being granted. Well done Maren! It will be exciting to follow Marens research the coming  years, which will focus on chromosomal inversions and evolutionary divergence in seaweed flies around the coasts of Scandinavia.

Last year Jessica Abbott got a similar grant, and it continues to go very well for young researchers both within our lab and in the rest of the Biology Department in Lund. I also encourage those of you who applied this year and did not get a grant (no one mentioned, but nobody forgotten), to not give up but try again next year. Competition is severe, and margins are often tight, but it is necessary to be persistent and believe in one's idéas. I, for myself, is also very happy and grateful that I got a grant this year, and I am looking forward to not have to apply for a while, but concentrate on research.

Lastly, I would like to congratulate former PhD-student Anna Runemark, who recently got one of her thesis-papers accepted in Molecular Ecology: a study on the relationship between inbreeding depression and secondary sexual character divergence in islant populations of Podarcis-lizards. I wish Anna all luck as she awaits the postdoctoral grant decisions from VR and EU/Marie Curie later this year. 

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

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.

New journal cover in Molecular Ecology: Vicariance divergence and gene flow among islet populations of an endemic lizard

I study genetic, morphological and behavioural divergence in islet populations of the Skyros wall lizard, Podarcis gaigeae. This species shows strong morphological divergence, including island gigantism (see the cover image, with adult male lizards from mainland populations to the left and islet populations to the right ). In this paper (found here) we have used isolation with migration models to investigate divergence times and levels of gene flow between islet populations and their closest mainland populations. Such background information is valuable for example for inferring rates of morphological and genetical divergence. Our results support that the studied islet populations have been sequentially separated by rising sea levels in the Aegean.

Abstract:

Allopatry and allopatric speciation can arise through two different mechanisms: vicariance or colonization through dispersal. Distinguishing between these different allopatric mechanisms is difficult and one of the major challenges in biogeographical research. Here, we address whether allopatric isolation in an endemic island lizard is the result of vicariance or dispersal. We estimated the amount and direction of gene flow during the divergence of isolated islet populations and subspecies of the endemic Skyros wall lizard Podarcis gaigeae, a phenotypically variable species that inhabits a major island and small islets in the Greek archipelago. We applied isolation-with-migration models to estimate population divergence times, population sizes and gene flow between islet–mainland population pairs. Divergence times were significantly correlated with independently estimated geological divergence times. This correlation strongly supports a vicariance scenario where islet populations have sequentially become isolated from the major island. We did not find evidence for significant gene flow within P. g. gaigeae. However, gene-flow estimates from the islet to the mainland populations were positively affected by islet area and negatively by distance between the islet and mainland. We also found evidence for gene flow from one subspecies (P. g. weigandi) into another (P. g. gaigeae), but not in the other direction. Ongoing gene flow between the subspecies suggests that even in this geographically allopatric scenario with the sea posing a strong barrier to dispersal, divergence with some gene flow is still feasible.