Formation of a new CAnMove action group: "Phenomics and visualization"

Most of us who are directly and indirectly involved in CAnMove were probably attracted to ecology and evolutionary biology because we were interested in organisms. Remember what organisms are? It is those big fluffy things, surrounding the genome called "birds", "mammals", "insects" and "fish" which you can see out in nature.

With the development of (admittedly powerful) new molecular tools, such as "Next-generation sequencing" and various genomic techniques, it seems, however, that biology and ecology have becoming increasingly reductionist disciplines. The appreciation for organisms and phenotypics traits have vaned, and partly been lost on the way. This is unfortunate, since next-generation sequencing has many pitfalls and problems. These techniques will certainly not solve all the remaining questions in ecology and evolutionary biology, in spite of frequent claims that it will.

As a matter of fact, ten years after the full sequence of the human genome was presented, there has been many disappointments,, and in spite of thousands of molecular markers developed for interesting human and highly heritable traits (e. g. height, diabetes etc.), only a tiny fraction of the heritable variation has been "picked up" and been detected by these thousands of molecular markers. This is called "The missing heritability problem" and refers to the fact that molecular and genomic techniques have been disappointly inefficient in explaining the abundant genetic variation in phenotypic traits, for both humans and other animals.

These disappointments from human genome research have certainly many practical consequences, as we are still very far from what was promised a decade ago that we would be able to have "personalized medicine" and individual treatments based on knowledge of individuals genotypes. Today, it is still much more efficient to predict an individuals probability of carrying certain genetic factors for a disease by asking them to fill out a questionary about their relative's disease history, than sequencing their genome!

This will also have some implications for studies of animal migration, including the search for so-called magic "migration genes". Even if such genes exist and even if we would be able to locate their genomic positions, the molecular markers that we will find will (at best) only explain a few percent of the phenotypic variation in migratory behaviour, except in unusual systems and circumstances. There is no reason that the search for such genes for interesting phenotypic traits in other animals will be different from the overall conclusion from studies of the human genome: most phenotypic adaptations are due to many genes of small effect size, and large-effect genes are the exceptions, rather than the rule. Quantitative genetics has, against what many predicted a decade ago, survived well and triumphed, as it is still the most efficient and cost-effective way of quantifying genetic variation in natural populations.

However, to move ecology and evolutionary biology forwards, we need also new and more efficeint ways of measuring and quantifying the phenotypes of organisms, whether those phenotypes are behavioural, morphological or physiological. This is the new and emerging field of phenomics as outlined by evolutionary geneticist David Houle in a couple of important articles (here and here) that will soon replace the more old-fashioned field of genomics. Well, perhaps phenomics will not replace genomics, but it will certainly complement its more reductionist enterprise. Ultimately, we want to understand phenotypes and how they evolve, and it is clear that genomics will not deliver as much as it was promised a decade ago. Phenomics aims to fill the missing knowledge gap here.

Phenomics is a collective name for the development of high-throughput phenotypic scoring and measurement techniques that can be used to rapidly quantify phenotypes, including 3D-laser scanning, data loggers to record behaviour and physiology, and various photographic and photometric techniques, e. g. thermal image cameras, of individuals under field conditions. These and other techniques will revolutionize our field in the future, in the same way like population genetics has been radically transformed by the vast information from genomics. The development of phenomics as a research field will require collaborations between ecologists, evolutionary biologists, physicists, engineers, computer scientists and programmers, like all other highly integrative research fields.

It is there clearly time that both CAnMove and Lund need to early get involved in the emerging field of phenomics, so that we do not get caught in yesterday's hat of genomics and are left behind the rapidly moving research front. For this reason, we have decided to form a new Action Group within CAnMove entitled "Phenomics and data visualization". Those of you who are interested in participating in this could contact me (erik.svensson@zooekol.lu.se) or CAnMove coordinator (susanne.akesson@zooekol.lu.se). The core of this group, apart from me and Susanne, will also be Anders Hedenström, but others who might want to join in should contact us with their idéas and suggestions.

CAnMove announces two new Stipends!

The titles of the two vacant Stipends are:

“Community metagenomics of Antarctic Protists – the importance of history versus environment”

and

“Immunological and physiological adaptations to migration: comparing migrating – sedentary populations and species”

The announcements are found at: http://www.naturvetenskap.lu.se/o.o.i.s/26278

Apply before 7th of March!

How did the Vikings navigate under cloudy skies?

In a recent paper published in Philosophical Transactions of the Royal Society B, CAnMove coordinator in collaboration with a team lead by an optical physicist Dr Gabor Horváth at Eötvös University in Budapest report on recent findings on how Viking navigators possibly could have used so-called sunstones to determine the position of the sun under foggy and cloudy conditions. The team for part of their work measured the skylight polarization under different optical conditions during an expedition (Beringia 2005) to the North Pole in 2005 organized by the Swedish Polar Research Secretariat. Based on these and additional measurements and psychophysical laboratory experiments we suggest that the optical physical conditions required for sun navigation by using sunstones are met under cloudy and foggy conditions, such that the pattern of skylight polarization are transmitted through the clouds and correspond to the pattern seen under clear sky conditions. Overall there is a reduction in degree of polarization of the incoming light under cloudy and foggy skies, but the pattern of skylight polarization is very similar to what is seen in a clear sky. It has been suggested that Vikings have used Icelandic spar (calcite) or possibly crystals of tourmaline, which are birefringent crystals (linearly polarizing crystals), to determine the Sun’s position when it could not be seen in the sky. It is a theory which has been discussed for a long time, however, still such sunstones have not been found in association with Shipwrecks from the Viking ages. Now we show that the optical prerequisites for sunstone navigation are met.

A more popular account of the recent findings is presented at e.g.
Nature News.

In the issue of Phil Trans also other work are presented from CAnMove scientist Rachel Muheim on polarization navigation in birds and by Marie Dacke and Eric Warrent in the Vision group at the Department of Biology at Lund University on the use of polarized light day and night-active insects.

Susanne

Identifying the migratory gene – new CanMove constellation

During the Häckeberga CanMove meeting in October, Staffan, Helena, Karin and Lasse started to discuss the possibility to use Daphnia pulex as an additional organism in CanMove´s search for “the migratory gene”. This organism is easily cultivated, produces a lot of cloned kids and, which is important, its genome is known. Later, when inspired by Steve Repperts talk on the Monarch butterflies during Miriam´s symposium on “Genetics of migration”, we decided to make this new initiative take real action. Our first steps have been to grow the organism and make some background search for information. So, in order to inform you all about this initiative, we hereby enclose a Christmas card from the lab. where the creatures are now reproducing and wishing us all a Merry Christmas and a Fruitful New year!

New paper on swift aerodynamics

A new paper based on wind tunnel research is just out. This time it is flapping flight of the swift Apus apus, which is investigated by means of high-speed Particle Image Velocimetry (PIV). The paper reveals many new details about the aerodynamics of this highly aerial bird. The main author is Per Henningsson, now a postdoc in the Oxford Animal Flight Group where he works on insect flight. Per did this work on swift flight together with Florian Muijres and Anders Hedenström as part of his PhD thesis that was entirely devoted to flight in the swift. Read about our favorite bird here.

CAnMove Symposium: "Genetics of Migration"

I believe that recent advances in the field of genomics will soon make it possible to evolve the research field of migration from phenotypic to molecular approaches to fully understand the genetic architecture of migratory traits. We thus considered this as an ideal point in time to provide a forum for researchers to exchange ideas and opinions on current research within the field of migratory genetics, and identify directions for future developments, and yesterday hosted the CAnMove Symposium on the "Genetics of Migration" in Lund.

We were indeed honoured by the number of participants, and excited to literally welcome participants from all over the world - thanks to you all having made this long trip to participate. It was great having had so many enthusiastic scientists - all working on one or the other aspect of the genetics of migration - here.

The backbone of the meeting was formed by six talks, presenting state-of-the-art research focussing on different aspects, covering a diverse range of taxa, and introducing methodological approaches that have recently emerged.

Steven Reppert from the University of Massachusetts shared insight into genomic, genetic and epigenetic approaches to monarch butterfly migration his lively lab is currently working on. Michael Banks from Oregon State University told us how genomics could help to elucidate spatiotemporal aspects of pacific salmon migration.

Within the field of migration, research on migratory birds has probably the longest tradition, and the talks of Martin Schaefer from Freiburg University and Staffan Bensch from Lund University focussed on microevolutionary processes and patterns of genetic and phenotypic variation along migratory divides in two migratory songbird species. Migratory divides as well as hybrid zones are great natural laboratories to study evolutionary processes and speciation, and the talks given by Anna Qvarnström and Jochen Wolf, both from Uppsala University, focussed on what we can learn from a Flycatcher hybrid zone, and how a genomic approach help us to incipient speciation in Carrion and Hooded crows.

Besides excellent talks, the highly interactive meeting included lively poster session and general discussions, sharing information and experience on the changes due to revolutionary technological achievements in this field. We closed the symposium with a plenary discussion evaluating methodological approaches to be focused upon, and critically assess possibilities and pitfalls thereof. The discussion also highlighted both importance and challenge of most accurately defining and controlling the target phenotype in focus, as well as including environmental variables in experimental design and analyses.

Discussion and plans for future projects, ideas for further development and collaboration continued over dinner – and will most certainly continue long thereafter.

On dispersal, gene flow, population divergence and learning in insects

                                                                            








One consequence of animal movement and dispersal is gene flow between populations. Gene flow is generally thought to limit local adaptation and population divergence, since local selection is opposed by the homogeneising effects of gene flow. In spite of this, we often find that populations differ in morphological, physiological and behavioural traits, and one way why such population divergence can be achieved is through adaptive phenotypic plasticity. In terms of behavioural traits, it is increasingly being recognized that learning can be important, particularly when it comes to population divergence of mate preferences.



We have studied the effects of learning on the development of female mate preferences in a charismatic insect species: the banded demoiselle (Calopteryx splendens). Males of different species in these calopotergid damselflies are well-known for their enigmatic melanized wing patches, which serve multiple ecological functions, including mate recognition and species recognition for females.

Recently, we have showed that female mate preferences are not entirely genetic, but are partly learned, and develops in females as a result of physical pre-mating interactions and/or during mating with males. The result of this learning is that populations that are even close to each other and hence experience a lot of gene flow in between them, can diverge substantially in mate preferences, due to such learning. It is interesting that even these small insects have such advanced cognitive ability so that they can actually learn whom to mate with, and who is the wrong mate! Our paper has recently been published in the journal Evolution, where we also contributed with the cover photo of a male banded demoiselle aggressively defending his valuable territory (a water lilly). Our article was also covered by the popular science site and media outlet Science Daily.

Below is the link to the article and the abstract:


A ROLE FOR LEARNING IN POPULATION DIVERGENCE OF MATE PREFERENCES  


Erik I. Svensson, Fabrice Eroukhmanoff, Kristina Karlsson, Anna Runemark & Anders Brodin

Article first published online: 13 JUL 2010

DOI: 10.1111/j.1558-5646.2010.01085.x

Learning and other forms of phenotypic plasticity have been suggested to enhance population divergence. Mate preferences can develop by learning, and species recognition might not be entirely genetic. We present data on female mate preferences of the banded demoiselle (Calopteryx splendens) that suggest a role for learning in population divergence and species recognition. Populations of this species are either allopatric or sympatric with a phenotypically similar congener (C. virgo). These two species differ mainly in the amount of wing melanization in males, and wing patches thus mediate sexual isolation. In sympatry, sexually experienced females discriminate against large melanin wing patches in heterospecific males. In contrast, in allopatric populations within the same geographic region, females show positive (“open-ended”) preferences for such large wing patches. Virgin C. splendens females do not discriminate against heterospecific males. Moreover, physical exposure experiments of such virgin females to con- or hetero-specific males significantly influences their subsequent mate preferences. Species recognition is thus not entirely genetic and it is partly influenced by interactions with mates. Learning causes pronounced population divergence in mate preferences between these weakly genetically differentiated populations, and results in a highly divergent pattern of species recognition at a small geographic scale.