Friday, February 22, 2013

Lab meeting on genetic diversity and climate change: What can we expect?

Anthropogenic climate change represents one of the biggest challenges and opportunities for ecologists and evolutionary biologists.

Oh wait. 

I mean modern genomics represents one the greatest challenges and opportunities for ecologists and evolutionary biologists. 

For those of us who thrive on challenges and opportunities, why not combine the two? As we don't know what future climate change will bring, and the possibilities for molecular ecology are constantly expanding, making predictions in this field can be difficult-- but also exciting. To provide some food for thought, I suggest that we read a recent invited review in Molecular Ecology at this week's lab meeting: 

Genetic diversity provides the basic substrate for evolution, yet few studies assess the impacts of global climate change (GCC) on intraspecific genetic variation. In this review, we highlight the importance of incorporating neutral and non-neutral genetic diversity when assessing the impacts of GCC, for example, in studies that aim to predict the future distribution and fate of a species or ecological community. Specifically, we address the following questions: Why study the effects of GCC on intraspecific genetic diversity? How does GCC affect genetic diversity? How is the effect of GCC on genetic diversity currently studied? Where is potential for future research? For each of these questions, we provide a general background and highlight case studies across the animal, plant and microbial kingdoms. We further discuss how cryptic diversity can affect GCC assessments, how genetic diversity can be integrated into studies that aim to predict species' responses on GCC and how conservation efforts related to GCC can incorporate and profit from inclusion of genetic diversity assessments. We argue that studying the fate of intraspecifc genetic diversity is an indispensable and logical venture if we are to fully understand the consequences of GCC on biodiversity on all levels.

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Also at this weeks' lab meeting, our newly arrived post-doc, Rachael Dudaniec, will give a short presentation on the topic of landscape genetics with examples from her recent work on mammals in Queensland, Australia (University of Queensland). Landscape genetics links landscape ecology and molecular genetic information to quantify the influence of landscape features on species’ dispersal. Landscape genetic patterns are sensitive to the focal species, the study location, and the time at which genetic information and landscape data were sampled.
Therefore, studies should be applied at spatial and temporal resolutions that are relevant for the focal species’ biology, while ideally providing meaningful outcomes for conservation managers. In this short talk, Rachael will outline the basics of landscape genetics and present recent analyses of landscape genetic connectivity in koalas and other small mammals in Australia that face threats from habitat fragmentation and urbanisation.

At Lund University, Rachael will work on adaptive landscape genomics and connectivity in Ischnura damselflies in relation to land use and climate change. 

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As usual, we meet at 10:30 on Tuesday (February 26) in Argumentet, and I will provide fika. Cheers, and see you there! -Lesley

New lab- and bloglogo made by Yuma Takahashi

Posted by Erik Svensson

You might notice that I have changed the lab-logo to a more fresh looking one, created by our postdoc Yuma Takahashi, who will unfortunately leave the lab next week to return to Japan, alongside with Natsu. We are of course grateful to both Yuma and Natsu for their contributions to the lab and we wish them good luck with their future research and careers.

Feel free to use this new logo yourself, in "Acknowledgements" after talks, for instance or when advertising things connected to EXEB.

Yuma was also kind enough to send me my name as written in Japanese, and I cannot resist the temptation to also post it below.

Saturday, February 16, 2013

Lab meeting about human evolution

For the lab meeting next week, I thought we should read a paper by Folmer Bokma (and others) "UNEXPECTEDLY MANY EXTINCT HOMININS," which asks "Did we humans kill our closest relatives?"


Recent studies indicate that Neanderthal and Denisova hominins may have been separate species, while debate continues on the status of Homo floresiensis. The decade-long debate between “splitters,” who recognize over 20 hominin species, and “lumpers,” who maintain that all these fossils belong to just a few lineages, illustrates that we do not know how many extinct hominin species to expect. Here, we present probability distributions for the number of speciation events and the number of contemporary species along a branch of a phylogeny. With estimates of hominin speciation and extincton rates, we then show that the expected total number of extinct hominin species is 8, but may be as high as 27.We also show that it is highly unlikely that three very recent species disappeared due to natural, background extinction. This may indicate that human-like remains are too easily considered distinct species. Otherwise, the evidence suggesting that Neanderthal and the Denisova hominin represent distinct species implies a recent wave of extinctions, ostensibly driven by the only survivor, H. sapiens.

Normal Time: Fika, Tuesday, 10.30 in Darwin.

Saturday, February 9, 2013

Workshop on "Behaviour and Speciation" in Oslo

This is a quick greeting and update from Oslo (Norway), where I have participated in a very stimulating research workshop entitled "Behaviour and Speciation", funded by FroSpects and organized by Glenn-Peter Saetre at CEES (Oslo). There were a number of interesting talks by invited speakers, including from Ole Seehausen, Lee Dugatkin, Darren Irwin and Anna Qvarnström, to mention only a few. It was nice to meet friends and colleauges like Darren who I have not seen for ten years, i. e. since he was postdoc in Lund.

It was also nice to meet former PhD-student Fabrice Eroukhmanoff (see picture above), who seems to be doing very well in his new research group and who now works in transgressive hybridization in a homoploid hybrid species of Passer-sparrow and its effects on various phenotypic traits, including beak morphology and beak allometry. Fabrice, Glenn-Peter and several others from the "Sparrow-group" gave several interesting talks about the ongoing work in this fascinating system where genomic, phenotypic and ecological data are now being put together to reveal a complicated but interesting speciation history.

I am writing this post from Fabrice's apartment in Oslo, where I am staying two nights before continuing to North Carolina and the NESCent-meeting about "Environmental determinants of selection". I was of course also pleased to hear that EXEB lab-member in Lund Jessica Abbott have been shortlisted for interview in her application for a "Startup Grant" for junior researcher to the European Research Council (ERC). Well done! An impressive achievement to make it this far, irrespective of the outcome during the interview in Brussels in April, I think.

Wednesday, February 6, 2013

Niko Tinbergen revisited

posted by Machteld

Niko Tinbergen is arguably the most famous Dutch biologist, having won a Nobel prize for his work on Animal Behaviour. As a Dutch student of animal behaviour, I have 'grown up' with his work, and  his work was taught even in my secondary school biology classes.  

He became a professor of biology at Leiden university after WWII, although he left for Oxford not long afterwards. By that point, he had already done some of his most famous work, including the study on instinct in herring gull chick, a study that he would write about quite a few times during his career, and is now a text book example of how certain stimuli can elicit 'instinctive behaviour' (as it was called at the time), and how some exaggerated stimuli elicit greater response than the natural stimuli do, a phenomenon well known as supernormal stimuli. Thus, this study has become very iconic in the field of behavioural biology.

Last week we discussed some occasions when iconic studies in biology were repeated, sometimes finding that the results are similar, but sometimes not. What does this mean for a particular field, when concepts have been built off of the results of such studies? 
This made me think of two papers that my PhD advisor, Carel ten Cate, wrote about the herring gull chick study of Tinbergen. Apparently, when Tinbergen left Leiden, he left behind some of his old field notes and material, including the original data sheets and the models he used in his experiments. I am not sure how they ended up in the hands of Carel, since the building we worked in was not build until after Tinbergen left Leiden, but I suspect that, thrifty as the university is/was, one particular piece of furniture, a set of drawers that was in Niko's office, was passed used in the then new building, and ended up in Carel's. But maybe I remember this wrong. In any case, Carel was of course very interested in these ‘artifacts’. After a while though, he started to investigate some of these findings more closely, and discovered some discrepancies between the original data sheets and the data that Tinbergen published.
Carel thought about what to do with this knowledge for a while, but over time, he decided it was important to publish this. He also started to incorporate some of these findings in his lectures. One year, some of his course students suggested that why not repeat the experiments with the original materials, and test if the ideas proposed by Tinbergen were true, even if the original data did not convincingly show this?
This resulted in two papers, which I suggest we read for next weeks’ lab meeting. The abstracts and links to the full papers you can find below. I think these two papers will supply us with some food for thought about scientific traditions, scientific conduct and the repeatability of experiments. In addition, I will also supply us with some actual food, for fika. 

Niko Tinbergen and the red patch on the herring gull's beak

One of the classic studies in animal behaviour is that by Niko Tinbergen on the stimuli that elicit begging behaviour in young herring gull, Larus argentatus, chicks. Tinbergen examined which features of the beak induced chicks to peck by using various cardboard models of herring gull heads in different shapes and colours. Leiden University, home university to Tinbergen at the time, still has a summarizing overview of the data of the initial experiment of the study. In that experiment, models with a yellow beak with patches in various colours and different positions were presented to young chicks. In this essay, I relate those earliest data to the various publications in which Tinbergen discussed them over the years. Subsequent publications became more and more detached from the original data, resulting in sizeable discrepancies between the original study and later descriptions of when and how the experiment was done and its outcome. I first sketch the scientific context of the herring gull study. Next I present the original data and document the subsequent changes. I discuss what might have led Tinbergen to modify his account of the study over the years, relating it both to its historical context and to the issue of ‘expectancy biases’.

Tinbergen revisited: a replication and extension of experiments on the beak colour preferences of herring gull chicks

Animal Behaviour Volume 77, Issue 4, April 2009, Pages 795–802

Young herring gull, Larus argentatus, chicks peck at the red patch on the lower mandible of their parent's yellow beak. In a famous study on the ‘instinctive behaviour’ of herring gull chicks, Tinbergen examined whether the presence, colour and position of the patch affected the pecking of the chicks. While this experiment is often cited as demonstrating a preference for a red patch, the original data showed that chicks pecked more at a black-patched model (Tinbergen 1948, De Levende Natuur51, 49–56). Tinbergen later ascribed this unexpected outcome to a methodological error in his experiment: the red-patched model was presented more frequently than all the others, which made him adjust his data later on. We repeated Tinbergen's experiment (experiment 1), using replicas of the original models. We also did the experiment as Tinbergen described it later on (but which he never carried out), presenting all models equally often (experiment 2). Our results confirm that red is not the most preferred colour when it is presented more often than other colours. In experiment 2 the relative ranking of all models was the same as in experiment 1, with the exception of the red-patched one, which was now preferred most, as expected by Tinbergen. Our findings also confirm that the more frequent exposure to the red model in experiment 1 resulted in a disproportionate decline in interest for this model. So, although he never did the actual experiment, Tinbergen's intuition and corrected data show a reasonable match to the results of our experiment.