Last EXEB-meeting in 2016 on December 20: hard and soft selection revisited

Posted by Erik Svensson

Nathalie and I decided to have a final EXEB-meeting of the year next week anyway, even though nothing was planned. Nathalie will bring "fika", and I will introduce a review paper (hopefully a light read) on "hard" and "soft" selection; two very important concepts that illustrate the difference between ecological and population genetic views of how selection works. Title and Abstract of the paper follows below.

When: Tuesday, December 20 at 10.00
Where: "Darwin, 2nd floor, Ecology Building

 Hard and Soft Selection Revisited: How Evolution by Natural Selection Works in the Real World

by David Reznick ( J Hered (2015) doi: 10.1093/jhered/esv07)

Abstract

The modern synthesis of evolutionary biology unified Darwin’s natural selection with Mendelian genetics, but at the same time it created the dilemma of genetic load. Lewontin and Hubby’s (1966) and Harris’s (1966) characterization of genetic variation in natural populations increased the apparent burden of this load. Neutrality or near neutrality of genetic variation was one mechanism proposed for the revealed excessive genetic variation. Bruce Wallace coined the term “soft selection” to describe an alternative way for natural selection to operate that was consistent with observed variation. He envisioned nature as presenting ecological vacancies that could be filled by diverse genotypes. Survival and successful reproduction was a combined function of population density, genotype, and genotype frequencies, rather than a fixed value of the relative fitness of each genotype. My goal in this review is to explore the importance of soft selection in the real world. My motive and that of my colleagues as described here is not to explain what maintains genetic variation in natural populations, but rather to understand the factors that shape how organisms adapt to natural environments. We characterize how feedbacks between ecology and evolution shape both evolution and ecology. These feedbacks are mediated by density- and frequency-dependent selection, the mechanisms that underlie soft selection. Here, I report on our progress in characterizing these types of selection with a combination of a consideration of the published literature and the results from my collaborators’ and my research on natural populations of guppies.

Praise for our book "The Adaptive Landscape in Evolutionary Biology"

As you hopefully remember, last year Ryan Calsbeek at Dartmouth College and I published an edited volume entitled "The Adaptive Landscape in Evolutionary Biology" (Oxford University Press 2012). Although we have generally gotten positive feedback and responses when talking research colleagues at meetings, relatively few reviews have yet appeared, probably because it is a relatively recent publication. Here is one very flattering review, however, published on the blog "Nothing in biology makes sense".

I thank the blog author for his kind words, and have to cite some of the nice formulations on a very long and thorough review:

"Unlike a recent book addressing aspects of the modern synthesis, Evolution: The Extendend Synthesis (Pigliucci and Müller, 2010) which called for a revolution, Svensson and Calsbeek have assembled authors that explore the innovations and contributions that build upon the fundamental ideas of population genetics and seek to grow the field. Early in this book, Pigliucci asks about the utility of the Adaptive Landscape metaphors, even titling his chapter with the question, “what are they good for?” I think the rest of the book provides a more than sufficient answer to his question."

and:

"Over the course of this semester, my colleagues and I read and discussed each of the chapters. Our group consisted of a diversity of backgrounds spanning evolution, ecology, and behavior. We included a range of experience from first and second year graduate students to postdocs as well as junior and senior faculty. While we read the book in the sequential order it was published in, each part could certainly be pulled out and read as a separately. Some of the chapters make cross references to each other but not enough that reading them independently would be impossible. While some chapters certainly provided more challenges to some, this forced our discussion to flesh out explanations that the text just didn’t have time to go into. I think that the first two parts might make particularly good set of readings to supplement an upper level Evolution or Population Genetics course."

and:

"My recommendationThis is a book ideally suited for a graduate level seminar in any Biology department. While it may be good to read a few chapters on your own, the book benefits from an active discussion of the content. We took 14 weeks to go through the entire book, reading one chapter most weeks occasionally two (or three). This pace allowed everyone to casually complete the readings. Going slowly through the book also allowed us to digest the material and make connections among the chapters without getting too overwhelmed with new information each week. You can follow this link to see the schedule we followed. If you are not convinced about the utility of this book yet, below I highlight some of the excellent contributions contained within the different parts."

and finally:

"CONCLUSION: I would strongly encourage students of population genetics to pick up this excellent volume and spend some contemplative weeks reading through the chapters. Better yet, grab a group of your department colleagues and argue about the 80 years of interpretation of the Adaptive Landscape. I personally cannot wait to see where this excellent metaphor leads us."

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.   

Welcome Lesley Lancaster, our new postdoc

I am pleased to welcome Lesley Lancaster, our new incoming postdoc, funded by BECC ("Biodiversity and Ecosystem Services in Changing Climate"). Lesley will arrive to Lund in late May or early June, and she will work with me and Bengt Hansson on the population genetics and ecology of range limit evolution, particularly using our favourite model organism: the damselfly Ischnura elegans ("Common Bluetail") as the main study object. Both Bengt and I are very excited about this project and about recruiting Lesley, who will bring with her new skills and perspectives from her previous research.

Currently, Lesley is a postdoctoral scholar at  the National Center for Ecological Analysis and Synthesis (NCEAS) in Santa Barbara (California, USA), where she has been since 2009. Her main focus of research has been to reconstruct historical evolutionary processes of adaptation, speciation, extinction and migration using time-calibrated molecular phylogenies of various Californian plant clades. She is also interested in historical habitat tolerances of the unique California chaparral habitat. Her postdoctoral research has resulted in some interesting papers in BMC Evolutionary Biology and Systematic Biology.

Lesley's thesis research was on a quite different topic: maternal effects, reproductive strategies and evolutionary ecology of a colour polymorphic lizard (Uta stansburiana), where she worked in the laboratory of Barry Sinervo at University of California, Santa Cruz (UCSC). Her thesis work also resulted in a number of interesting and impressive publications in American Naturalist, Ecology Letters, Evolution and PNAS. 

Lesley is thus an extremely broad and well-rounded biologist and a very experienced postdoc, who has worked at quite different levels of biological organization, and moved her research focus from studies of individual behaviour and evolutionary ecology, to broader macroevolutionary and macroecological questions. It is for precisely these reasons we are excited to bring her in to Lund; she has both sufficient much in common with our already ongoing research,  yet has many complementary skills that will be of interest to us and our research.

On "Evolutionary rescue", climate change and evolution of range limits

This week the lab-meeting will focus on  "Evolutionary rescue", which was a topic of a recent scientific conference involving several leading evolutionary biologists and ecologists in France, including leading population geneticist Mark Kirkpatrick who gave a talk entitled: "The evolution of a species’ range by beneficial mutations". 

The organisers of this interesting conference has been kind enough to put up videos on the internet of Mark's talk, which you can find here, as well as two other interesting talks by contributors. This is an excellent way of making it possible for others, like us, who could not take part in this meeting, and also a very environmentally-friendly way of spreading scientific information without necessarily travelling to every meeting you wish to attend.

I suggest that we meet the usual time (13.30 on Wednesday April 15 in "Argumentet") to listen to Mark's talk, and (if we have time), to one or two of the other talks. Thus, there is no need to read any paper before this lab-meeting, just come sharp and alert and be willing to discuss! Hopefully, we can arrange with Machteld's computer to be linked to the Powerpoint-projector so we can see the talk on a large screen. 

 

Lab-meeting on the history of the Adaptive Landscape

For next week's lab-meeting, we'll become more philosophical and historical, and discuss a book chapter about the history of the Adaptive Landscape metaphor in evolutionary biology. This chapter will be one of approximately 20 chapters in a forthcoming volume at Oxford University Press that I am currently editing together with my colleague Ryan Calsbeek (Dartmouth College, New Hampshire, USA).

This volume is intended to become published in 2012, which marks the 80-year celebration of population geneticist Sewall Wright's famous paper in 1932 where the concept of the Adaptive Landscape was first explicitly presented. Both Ryan and I are looking forward to input on this chapter, and in case you have not received a copy prior to our lab-meeting and wish to participate, send me an e-mail (erik.svensson@zooekol.lu.se). Time and location for lab-meeting as usual: "Darwin" at 13.30-15.00 on March 2, 2011. Fika volunteers are most welcome!

Papers for labmeeting on November 24: genomics and sex ratio evolution

This Wednesday, we will discuss two short papers, one in Nature Genetics and the other one in Nature. They are both very short, but should make interesting reads. The first paper was suggested by Bengt Hansson, and is an example of how the sequencing of entire genomes can shed light over local adaptation, in this case of the plant Arabdopsis lyrata to serpentine soils. You can download that paper here. The second paper is an example of how climatic factors can drive population divergence in sex determination systems, in this case over an altitudinal gradient of an Australian lizard species. You can download that paper here. Abstracts of both papers are provided below.

I hope you enjoy these papers and that we will have a good discussion. Time and place as usual: "Darwin" at 10.15 (Wednesday November 24). Fika volunteers are encouraged to step forward.

Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils  

Thomas L Turner, Elizabeth C Bourne, Eric J Von Wettberg, Tina T Hu & Sergey V Nuzhdin

Nature Genetics 42: 260–263 (2010)

DOI: doi:10.1038/ng.515

A powerful way to map functional genomic variation and reveal the genetic basis of local adaptation is to associate allele frequency across the genome with environmental conditions. Serpentine soils, characterized by high heavy-metal content and low calcium-to-magnesium ratios, are a classic context for studying adaptation of plants to local soil conditions. To investigate whether Arabidopsis lyrata is locally adapted to serpentine soil, and to map the polymorphisms responsible for such adaptation, we pooled DNA from individuals from serpentine and nonserpentine soils and sequenced each 'gene pool' with the Illumina Genome Analyzer. The polymorphisms that are most strongly associated with soil type are enriched at heavy-metal detoxification and calcium and magnesium transport loci, providing numerous candidate mutations for serpentine adaptation. Sequencing of three candidate loci in the European subspecies of A. lyrata indicates parallel differentiation of the same polymorphism at one locus, confirming ecological adaptation, and different polymorphisms at two other loci, which may indicate convergent evolution.

Climate-driven population divergence in sex-determining systems

Ido Pen, Tobias Uller, Barbara Feldmeyer, Anna Harts, Geoffrey M. While & Erik Wapstra

Nature 468: 436–438 (18 November 2010)

DOI: doi:10.1038/nature09512

Sex determination is a fundamental biological process, yet its mechanisms are remarkably diverse. In vertebrates, sex can be determined by inherited genetic factors or by the temperature experienced during embryonic development. However, the evolutionary causes of this diversity remain unknown. Here we show that live-bearing lizards at different climatic extremes of the species’ distribution differ in their sex-determining mechanisms, with temperature-dependent sex determination in lowlands and genotypic sex determination in highlands. A theoretical model parameterized with field data accurately predicts this divergence in sex-determining systems and the consequence thereof for variation in cohort sex ratios among years. Furthermore, we show that divergent natural selection on sex determination across altitudes is caused by climatic effects on lizard life history and variation in the magnitude of between-year temperature fluctuations. Our results establish an adaptive explanation for intra-specific divergence in sex-determining systems driven by phenotypic plasticity and ecological selection, thereby providing a unifying framework for integrating the developmental, ecological and evolutionary basis for variation in vertebrate sex determination.

Genetics of pygmy evolution in Africa

Some of you might be interested in a recent study about the evolutionary origins of African human pygmy populations, which is discussed in this bloggpost. A recent study have investigated the molecular genetic history of African pygmy populations and concluded that they are not secondarily derived from the farming populations of the Bantu people. Instead, the different and the isolated pygmy populations in the African rainforests are historical relicts of a greater contiguous population of an ancestral hunter-gather society that was split up in to different fragmented populations when the African Bantu people expanded about 10 000 years ago.

The different pygmy populations in Africa have thus not evolved their short body stature in parallel. Rather their phenotypic traits are traits that they inherited from their ancestors. The pygmy populations and the Bantu people have been separated for at least 60 000 years. The agricultural revolution took place the last 10 000 years, and when the Bantu people brought agriculture to sub-saharan Africa, their population sizes exploded. This is because the carrying capacity of agricultural populations is considerably higher than for hunter-gather societies. which is not very surprising. After all, by using agriculture you can feed a much larger population per unit area than you could by hunting.

The pygmies were thus marginalized by the rapidly expanding Bantu-farmers, and their once large population was split up in to several smaller fragmented populations. The once more widespread pygmies are today more less isolated from each other in the deep African rainforest.

As an aside, this is an interesting example of how population genetics, particularly the use of the population genetic software STRUCTURE, can be fruitfully used to infer population histories and population genetic parameters (see figure above). This is something we are also working on in our laboratory, particularly Anna in her studies of Mediterranean Podarcis-lizards.