Friday, February 12, 2016

Is Plasticity facilitating or impeding Adaptive Evolution?

Again. I know that we discussed this topic not too long ago, but I feel that the issue is not satisfyingly resolved and I got a bit stuck with it... Therefore, I would like to discuss a paper by Dayan et al., 2015, Mol Ecol, that tackles this controversy. The authors are trying to assess the role of phenotypic plasticity in evolution by comparing gene expression patterns in killifish (Fundulus spp.). They are contrasting divergent populations and test to what extent their ability to acclimate to different temperatures varies. They address questions such as whether plasticity and genetic divergence operate in parallel on the same set of genes, or what the magnitude of the plastic response is compared to the evolved response. I think these are exciting questions and I hope you enjoy reading the paper and discussing their ideas (don't get scared by the stats!).

Link to the paper is here and there is also a little commentary on it here.

When: Tuesday, 16th of Feburuary 2016, 10 am
Where: Argumentet

Title: Phenotypic plasticity in gene expression contributes to divergence of locally adapted populations of Fundulus heteroclitus
Abstract: We examine the interaction between phenotypic plasticity and evolutionary adaptation using muscle gene expression levels among populations of the fish Fundulus heteroclitus acclimated to three temperatures. Our analysis reveals shared patterns of phenotypic plasticity due to thermal acclimation as well as non-neutral patterns of variation among populations adapted to different thermal environments. For the majority of significant differences in gene expression levels, phenotypic plasticity and adaptation operate on different suites of genes. The subset of genes that demonstrate both adaptive differences and phenotypic plasticity, however, exhibit countergradient variation of expression. Thus, expression differences among populations counteract environmental effects, reducing the phenotypic differentiation between populations. Finally, gene-by-environment interactions among genes with non-neutral patterns of expression suggest that the penetrance of adaptive variation depends on the environmental conditions experienced by the individual.

...and yes, there will be fika :-)

Friday, February 5, 2016

Lab Meeting on Ancient Microbiomes

Posted by Katie Duryea

This week for lab meeting I thought it might be fun to read this recent paper that explores the gut microbiome of the Iceman mummy to draw inference on the evolutionary history of human stomach ailments. I'll bring some fika that will hopefully sit well with your microbiome;)

When: Tues, February 9th, 10:00
Where: Argument

The 5300-year-old Helicobacter pylori genome of the Iceman

  • Frank Maixner 1 , * , , 
  • Ben Krause-Kyora 2 , , 
  • Dmitry Turaev 3 ,
  • Alexander Herbig 4 , 5 ,
  • Michael R. Hoop Mann 6 ,
  • Janice L. Hallow 6 , 
  • Ulrike Kusebauch 6
  • Eduard Egarter Vigl 7
  • Peter Malfertheiner 8
  • Francis Megraud 9 ,
  • Niall O'Sullivan 1
  • Giovanna Cipollini 1
  • Valentina Coia 1
  • Marco Samadelli 1
  • Lars Engstrand 10
  • Bodo Linz 11 ,
  • Robert L. Moritz 6
  • Rudolf Grimm 12
  • John Krause 4 , 5 ,
  • Almut Nebel 2 ,
  • Yoshan Moodley 13 , 14 ,
  • Thomas Rattei 3 ,
  • Albert Zink 1 , *

  • Abstract

    The stomach bacterium Helicobacter pylori is one of the most prevalent human pathogens. It has dispersed globally with its human host, resulting Thing thing into a distinct phylogeographic pattern That Can Be Used to Reconstruct bothering Recent and ancient human migrations. The extant European populations of H. pylori is known to be a hybrid between Asian and African bacteria, but there exist different Hypotheses about When and Where The hybridization took place, reflecting the complex demographic history of Europeans. Here, we present a 5300-year-old H. pylori genome from a European Copper Age glacier mummy. The "Iceman" H. pylori is a nearly pure representative of the bacterial population of Asian origin That existed in Europe before hybridization, suggesting That the African population arrived in Europe within the past few thousand years.        
  • Sunday, January 31, 2016

    Half-time seminar on micro- and macroevolution by PhD-student John Waller (February 2, 13.00)

    John Waller

    Posted by Erik Svensson 

    As you already hopefully know, we will have our regular EXEB meeting in the morning of February 2 on the topic "Can the evoutionary process learn?", and it is Tobias Uller who organizes this interesting seminar. 

    Later the same day, in the afternoon, there is another interesting EXEB-event: one of the PhD-students in the EXEB environment (John Waller), will have his half-time seminar with the following title:

    "Connecting microevolutionary processes and macroevolutionary patterns in damselflies and dragonflies"

    Locale: "Red Room", Ecology Building
    Date and time: Tuesday, February 2, 13.00 

    As many intern students, field and lab assistants have helped John to collect data for his PhD-work, we wish all those and others within and outside the EXEB-environment most welcome to this interesting seminar. Dr. Lars Råberg (Functional Zoology Unit), will be the opponent on John's half-time seminar and report. 

    Friday, January 29, 2016

    Can the Evolutionary Process Learn?

    Posted by Tobias Uller

    Next week I thought we would discuss an opinion piece in TREE by Richard Watson and Eörs Szathmary. The thought-provoking suggestion - based on insightful use of learning theory - is that the basic ingredients of evolution (organismal variation, differential reproductive success, and inheritance) evolve in ways that make evolution a more directed process than we might think. Richard and Eörs explain the basics and apply the logic to evolvability, ecosystems and major transitions.

    Paper can be found here, abstract below.

    Time: Tuesday, Feb 2, at 10.00

    Where: "Argumentet", 2nd floor, Ecology Building
    Coffee guaranteed and there is a decent chance of kanelbulle
    The theory of evolution links random variation and selection to incremental adaptation. In a different intellectual domain, learning theory links incremental adaptation (e.g., from positive and/or negative reinforcement) to intelligent behaviour. Specifically, learning theory explains how incremental adaptation can acquire knowledge from past experience and use it to direct future behaviours toward favourable outcomes. Until recently such cognitive learning seemed irrelevant to the ‘uninformed’ process of evolution. In our opinion, however, new results formally linking evolutionary processes to the principles of learning might provide solutions to several evolutionary puzzles – the evolution of evolvability, the evolution of ecological organisation, and evolutionary transitions in individuality. If so, the ability for evolution to learn might explain how it produces such apparently intelligent designs.

    Saturday, January 23, 2016

    Jan. 26th: Major evolutionary transitions

    Posted by Jessica Abbott

    For the next meeting I've chosen a paper about one of the big ideas in evolutionary biology, that of the major evolutionary transitions during the history of life. This paper examines under what conditions a major evolutionary transition can occur.

    Title: Major evolutionary transitions in individuality

    Abstract: The evolution of life on earth has been driven by a small number of major evolutionary transitions. These transitions have been characterized by individuals that could previously replicate independently, cooperating to form a new, more complex life form. For example, archaea and eubacteria formed eukaryotic cells, and cells formed multicellular organisms. However, not all cooperative groups are en route to major transitions. How can we explain why major evolutionary transitions have or haven’t taken place on different branches of the tree of life? We break down major transitions into two steps: the formation of a cooperative group and the transformation of that group into an integrated entity. We show how these steps require cooperation, division of labor, communication, mutual dependence, and negligible within-group conflict. We find that certain ecological conditions and the ways in which groups form have played recurrent roles in driving multiple transitions. In contrast, we find that other factors have played relatively minor roles at many key points, such as within-group kin discrimination and mechanisms to actively repress competition. More generally, by identifying the small number of factors that have driven major transitions, we provide a simpler and more unified description of how life on earth has evolved. 

    Time and place: 10:00-11:00 January 26th, in Argumentet

    Thursday, January 14, 2016

    Spring 2016 semester schedule for EXEB-meetings

    Posted by Erik Svensson

    Following a Doodle poll about which dates EXEB-members would be present and could participate and take care in organizing our regular (weekly) Tuesday-meetings, I have now put together a tentative schedule for spring 2016. Everybody except one has participated in this poll, and I have now allocated you dates based on this poll.

    As usual, the person(-s) responsible for organizing a meeting decide the activitiy, which is often (although not always) to discuss an interesting scientific paper or, alternatively, to give a short (informal) presentation of ongoing research. Also as usual, it is a the person(-s) responsible who will write a blog post, announcing the theme of the meeting. Ideally, this blog post should be up on Thursday or Friday the week before, particularly if it is a paper to be discussed, as people will need time to digest the material. 

    Note that, although we are quite many now in the EXEB-environment, some of us will have to arrange two meetings this semester to fill the slots, which is hopefully not too painful.

    Also, feel free if you have a visitor to let him/her present his research in this informal and relaxed scientific environment. If you have to cancel your slot, make sure you find a substitute or swich date with someone else on the list.

    EXEB schedule spring 2016 (tentative and subject to change)

    Tuesday, January 19: Erik Svensson

    Tuesday, January 26: Jessica Abbott

    Tuesday, February 2: Tobias Uller

    Tuesday, February 9: Katie Duryea

    Tuesday, February 16: Nathalie Feiner

    Tuesday, February 23: Katrine Lund-Hansen

    Tuesday, March 1: John Waller

    Tuesday, March 8: Reinder Radersma

    Tuesday, March 15: Talk by Wiebke Feindt (host: Erik Svensson)

    Tuesday, March 22: Hanna Laakonen

    Tuesday, March 29: Weizhao Yang

    Tuesday, April 5: Anna Nordén

    Tuesday, April 12: Beatriz Willink

    Tuesday, April 19: Antonio Cordero

    Tuesday, April 26: Erik Svensson

    Tuesday, May 3: Jessica Abbott

    Tuesday, May 10: Tobias Uller

    Tuesday, May 17: Katie Duryea

    Tuesday, May 24: Nathalie Feiner

    Tuesday, May 31: Katrine Lund-Hansen

    First EXEB-meeting in 2016: on speciation, ecological opportunity and latitude


    Crab spider (Misumenia vatia) with prey. Photo: Erik Svensson

    Posted by Erik Svensson 

    "Evolution in Sweden 2016" is now over, and in my opinion it was a great success. You can see photos from this meeting here, and we can also briefly summarize our general reflections about this meeting on the first EXEB-meeting, which I post information about below. 

    On this first EXEB-meeting of 2016, I want to discuss a recent paper published as a "Presidential Adress" in American Naturalist by Dolph Schluter, entitled "Speciation, ecological opportunity and latitude". 

    I saw Dolph give a talk about this last year at a speciation-meeting in California, and I think that he is a very thoughtful scientist who has stimulated my thinking and influenced many other ecologists and evolutionary biologists. Hopefully, we will have a good discussion about this paper. But as usual, we will start the meeting with some general reflections, summary of impressions of "Evolution in Sweden 2016" and we can also hear a bit from Tobias and Nathalie's trip to Australia, as well as mine, Katie's and John's trip to Argentina. I might even bring some pictures to show. 

    Time: Tuesday, January 19, at 10.00

    Where: "Argumentet", 2nd floor, Ecology Building

    Abstract: Evolutionary hypotheses to explain the greater numbers of species in the tropics than the temperate zone include greater age and area, higher temperature and metabolic rates, and greater ecological opportunity. These ideas make contrasting predictions about the relationship between speciation processes and latitude, which I elaborate and evaluate. Available data suggest that per capita speciation rates are currently highest in the temperate zone and that diversification rates (speciation minus extinction) are similar between latitudes. In contrast, clades whose oldest analyzed dates precede the Eocene thermal maximum, when the extent of the tropics was much greater than today, tend to show highest speciation and diversification rates in the tropics. These findings are consistent with age and area, which is alone among hypotheses in predicting a time trend. Higher recent speciation rates in the temperate zone than the tropics suggest an additional response to high ecological opportunity associated with low species diversity. These broad patterns are compelling but provide limited insights into underlying mechanisms, arguing that studies of speciation processes along the latitudinal gradient will be vital. Using threespine stickleback in depauperate northern lakes as an example, I show how high ecological opportunity can lead to rapid speciation. The results support a role for ecological opportunity in speciation, but its importance in the evolution of the latitudinal gradient remains uncertain. I conclude that per capita evolutionary rates are no longer higher in the tropics than the temperate zone. Nevertheless, the vast numbers of species that have already accumulated in the tropics ensure that total rate of species production remains highest there. Thus, tropical evolutionary momentum helps to perpetuate the steep latitudinal biodiversity gradient.