Evolutionary Ecology

The Division of Evolutionary Ecology is interested in understanding both the proximate genetic mechanisms and ultimate ecological causes of evolutionary processes, such as adaptation to divergent environments, the formation of new species, and the evolution of sex chromosomes. Our main model system is a small fish called the threespine stickleback (Gasterosteus aculeatus) and its close relatives in the stickleback family (Gasterosteidae). These fish have adapted to a variety of marine and freshwater habitats across the Northern hemisphere and consequently evolved incredible diversity in their behaviors, morphologies, life histories, and sex chromosomes on a relatively short evolutionary time scale. The development of genetic and genomic tools for these fish has allowed us to identify specific genetic, genomic, and molecular changes that underlie this phenotypic diversity and that contribute to reproductive isolation between phenotypically and ecologically divergent populations.

News

Dr. Ariel Ruiz Urquiola receives Scholars at Risk grant

Congratulations to Dr. Ariel Ruiz Urquiola, who received a Scholars at Risk grant from the Swiss National Science Foundation to support his project "Speciation Processes and Population Dynamics (Diversity and Migration) in the Fragmented Karsts of the ‘Sierra de los Organos’, Western Cuba". In this project, Ariel will continue his work on understanding the evolution of both invertebrate and vertebrate species found in the Sierra de los Organos karst system in Cuba. He has collected genetic and phenotypic data from nearly 15,000 samples from 150 locations and will now have the opportunity to analyze and publish his very interesting data. We are very grateful to the SNSF and the University of Bern for their support, which will enable Ariel to reestablish his academic career after being expelled from Cuba for his political activities.

Congratulations Dr. Carlos Rodríguez-Ramírez

Congratulations to Dr. Carlos Rodríguez-Ramírez, who successfully defended his thesis entitled “Eda, gene pathways and alternative splicing: the genetic basis of adaptive evolution in threespine stickleback”. Carlos gave a great talk and followed it with a fun discussion. Special thanks to Kathryn Elmer for serving as the external examiner and Claudia Bank for chairing the defense, as well as Araxi Urrutia for co-supervision of Carlos during his PhD. We will miss Carlos, his ideas and questions, and his generous and positive attitude. But, happily, he will just be down the road from us, doing his postdoc at the University of Lausanne.

Can we predict speciation?

In honor of the precisely predicted total solar eclipse that indeed occurred today in North America, Marius Roesti and colleagues explore the question of whether speciation is predictable. In a new paper for the Cold Spring Harbor Perspectives in Speciation volume, Marius and colleagues explore the general limits of predictability, the value of making predictions, and how to move from hypothesis to a predictive model of speciation. Check it out for a fun and thought-provoking read (and to learn what an orrery is). If you are interested in discussing the topic of predictability in evolutionary biology, check out the symposium "Empirical and Conceptual Insights
on the (Un)Predictability of Evolution" that Marius is organizing at the upcoming Joint Congress on Evolutionary Biology in Montreal!

Majda Bohutínská wins the John Maynard Smith Prize from the European Society for Evolutionary Biology!

Dr. Magdalena (Majda) Bohutínská, a Marie Skłodowska-Curie Actions postdoctoral fellow in the Division of Evolutionary Ecology and at Charles University in Czechia, has won the 2024 John Maynard Smith Prize from the European Society for Evolutionary Biology (ESEB)! This prize recognizes an outstanding young evolutionary biologist and is named after John Maynard Smith, an eminent evolutionary biologist and former President of ESEB. Majda's unlimited creativity, energy and enthusiasm for biology are an inspiration for all of us, and we are very lucky to have her as our colleague here in Bern! Majda will give the 2024 John Maynard Smith Prize Lecture at the next joint Evolution meeting, held in July 2024 in Montreal, Canada.

Divergence time shapes gene reuse during repeated adaptation

Majda Bohutínská led a new review that appears in the April 2024 issue of Trends in Ecology & Evolution. In this review, she analyzed nearly 30 case studies in which independent lineages have repeatedly responded to similar environmental changes ('repeated adaptation'). She finds that divergence time among lineages is a key factor driving the extent to which the same genes are involved in repeated adaptation ('gene reuse'). Specifically, more recently diverged lineages exhibit higher gene reuse. Majda proposes that this is likely because as lineages diverge, there is a reduction in allele sharing, functional divergence among genes, and changes in genome architecture. However, she highlights that the relationship between gene reuse and divergence time is complex, and that more work in needed in the future to predict the genetic basis of adaptation. Her beautiful review is accompanied by a beautiful cover image of Majda's favorite study system Arabidopsis arenosa, in which three mostly lowland lineages (bottom row) have repeatedly adapted to the alpine environment (top row). It's not sticklebacks, but still pretty cool!

Big Biology Podcast on experimental evolution in the wild

The Big Biology Podcast is doing a series of podcasts on our big experimental evolution project, in which we put over 10,000 sticklebacks into nine real lakes in Alaska! We recently got an SNSF Advanced Grant to sequence the genomes of every one of these founding fish so that we can track how genotypes and phenotypes change over time. Check out the first podcast in the series featuring a discussion with Katie and Andrew Hendry (McGill University) to learn more about the project and the need for long-term experimental studies of evolution in the wild!

Dr. Zuyao Liu successfully defends his PhD

Congratulations to Dr. Zuyao Liu, who successfully defended his thesis entitled “Exploring the Evolutionary Significance of Chromosomal Fusions and Inversions: Implications for Adaptive Evolution and Sex Chromosome Evolution”. Zuyao gave a beautiful talk and impressed his defense committee with his thoughtful answers to their questions. Special thanks to Qi Zhou for serving as the external examiner and Claudia Bank for chairing the defense, as well as Sam Yeaman for co-supervision of Zuyao during his PhD. After a well-deserved vacation in China, Zuyao will start a new adventure as a postdoc studying the role of inversions in adaptation. Lucky for us, he will stay right here in the Division of Evolutionary Ecology!

Katie Peichel elected to the US National Academy of Sciences

Today Katie learned that she was elected by her peers to the US National Academy of Sciences “in recognition of her distinguished and continuing achievements in original research”. It is an amazing honor, not only for her, but for all the technicians, bachelors students, masters students, PhD students, postdoctoral fellows, and collaborators who have brought their creativity, ideas, passion and hard work to our group for the past 20 years!!! Together we have done some great science, and most importantly, we had fun doing it while caring for each other! And, we are not done - the best is yet to come…

Phenotypic species divergence driven by resource competition and shared predation

In a new paper published in Ecology Letters, Marius Roesti and colleagues compared co-occurring (sympatric) and allopatric populations of both threespine stickleback and prickly sculpin fish. They find phenotypic shifts in opposite direction between the species when sympatric. These shifts are seen in typical trophic traits and diet, as well as in traits providing protection against predation. This study suggests that ecological character displacement driven by resource competition has increased vulnerability of one species but decreased vulnerability of the other species to a shared predator (trout). Overall, this study highlights the importance of the indirect interaction via shared predators for driving divergence between prey species.

Two Bernese researchers receive SNSF Advanced Grant

Neuropsychologist Katharina Henke and evolutionary biologist Katie Peichel are each receiving a highly endowed SNSF Advanced Grant from the Swiss National Science Foundation (SNSF). Their research projects deal with the ability to remember despite amnesia and the predictability of evolution.

Happy Birthday Gregor Mendel!

In honor of the 200th birthday of Gregor Mendel, who discovered the genetic mechanism of the inheritance of traits, the Proceedings of the National Academy of Sciences USA has created a Special Feature with a collection of articles focusing on the impact of Mendel on modern evolutionary biology. Together with Kirsten Bomblies, Katie wrote a review on the genetics of adaptation. Check out the review, which is accompanied by Kirsten's beautiful drawings of model systems in evolutionary genetics, including of course the threespine stickleback!

Global Urban Evolution Project published in Science

During their time as postdocs in the Division of Evolutionary Ecology, Matt Josephson, Diana Rennison, and Matt Zuellig collected white clover from a urban to rural cline in Bern as part of the Global Urban Evolution project led by Marc Johnson at the University of Toronto. A paper describing the results of this worldwide study, based on 110,019 plants from 6169 populations in 160 cities from 26 countries was just published in Science. This large dataset demonstrates that adaptation to urban environments drives the evolution of hydrogen cyanide production (an antiherbivore chemical defense) and further identifies specific environmental factors that influence whether urban-rural clines evolve in parallel. Glad that we could make a small contribution to such a cool project!

The Ecology and Biogeography of Sri Lanka: A context for freshwater fishes

Hiranya Sudasinghe, a joint PhD student with Lukas Rüber at the Natural History Museum of Bern, has published a book! Despite advances in biodiversity exploration, the origins of Sri Lanka's fauna and flora have never yet been treated in a synthetic work. This book draws together the threads that make up that fascinating 100-million year story. Encompassing the island's entire biota while emphasising the ecology, biogeography and phylogeography of freshwater fishes, it provides a comprehensive context for understanding how the island's plants and animals came to be as they are. The 258-page text contains more than 200 figures, photographs and maps. It provides a clear account of how, when and from where the ancestors of the plants and animals that now inhabit Sri Lanka came. For the first time, the island's unique biodiversity can be understood and appreciated in its historical and evolutionary context in this invaluable sourcebook, designed for scientists, students and biodiversity enthusiasts alike.

Katie Peichel elected to the American Academy of Arts and Sciences

Today the American Academy of Arts and Sciences announced the election of 276 artists, scholars, scientists, and leaders in the public, non-profit, and private sectors, including Professor Catherine (Katie) Peichel!

Academy members are world leaders in the arts and sciences, business, philanthropy, and public affairs. They are based across the United States and around the world. Current Academy members represent today’s innovative thinkers in every field and profession, including more than two hundred and fifty Nobel and Pulitzer Prize winners. Katie is beyond honored and humbled to be included in the long list of distinguished members, including international honorary members Albert Einstein and Charles Darwin!

Founded in 1780, the American Academy of Arts and Sciences honors excellence and convenes leaders from every field of human endeavor to examine new ideas, address issues of importance to the nation and the world, and work together “to cultivate every art and science which may tend to advance the interest, honor, dignity, and happiness of a free, independent, and virtuous people.”

About the distribution of biodiversity on our planet

Dr. Marius Roesti of the Division of Evolutionary Ecology led a study published in Nature Communications that challenges a long-standing explanation for the distribution of biodiversity on our planet. Since Charles Darwin, biologists have been using the so-called "biotic interactions" hypothesis to explain, at least in part, why the tropics around the equator are so species rich. The hypothesis focuses on the importance of interactions between species for biodiversity and is intuitively appealing: the stronger the interactions between species, the faster evolutionary change, thus resulting in increased species diversity. Testing this long-standing hypothesis has proven extremely difficult in the past, and the results from past studies are mixed. This publication in Nature Communications now further challenges the general validity of the "biotic interactions" hypothesis. The study suggests that a specific but fundamental interaction between species – predation by large fish such as tunas or sharks – is stronger in the temperate zone than near the equator. According to the "biotic interactions" hypothesis, stronger interactions should be accompanied by a higher diversity of fish species – a pattern that is also not born out by the study. Marius began the research work while a postdoctoral fellow at the University of British Columbia in Vancouver and completed it after moving to the University of Bern.

Katie Peichel is an author on the new edition of the Introduction to Genetic Analysis textbook

The 12th edition of the Introduction to Genetic Analysis textbook has just been released. Katie Peichel revised and updated the chapters on Genetics and Genomics, Developmental Genetics, Chromosomal Changes, and Evolution. She added content on next-generation sequencing methods and analyses, as well as an evolutionary perspective on genetic analyses in non-traditional model organisms throughout these chapters. Katie was honoured to be an author on the same textbook (5th edition) she used as an undergraduate studying genetics at UC Berkeley many years ago!

Convergent evolution in the genomics era

A special issue of the Philosophical Transactions of the Royal Society B was published today on the identification of the genomic factors underlying convergent evolution, i.e. the evolution of similar phenotypes in independent lineages. Dr. Diana Rennison led a study published in this special issue. In collaboration with Katie Peichel, Dan Bolnick and Yoel Stuart (University of Texas, Austin), she identified both ecological factors and morphological traits associated with genomic regions that are repeatedly differentiated across 16 independently evolved pairs of lake and stream sticklebacks from Vancouver Island, British Columbia, Canada. This study highlights the importance of including ecological and morphological data in population genomic studies to identify links between genotypes, phenotypes and fitness.

Science paper - A key metabolic gene for recurrent freshwater colonization and radiation in fishes

What factors contribute to colonization of new ecological niches? To address this question, Asano Ishikawa and Jun Kitano (National Institute of Genetics, Japan) led a collaboration that included the Divisions of Evolutionary Ecology and Aquatic Ecology & Evolution in the IEE, and our colleagues at Eawag. Together we demonstrated that there have been multiple independent duplications of a gene required for fatty acid biosynthesis in lineages of fish that have successfully colonized freshwater, but not in lineages that have failed to do so. Genetic studies in threespine stickleback demonstrate that this duplication increases survival in freshwater diets that lack essential fatty acids, suggesting that this gene duplication contributed to the ability of fish to invade nutrient poor freshwater habitats.

Dr. Matt Zuellig wins the 2019 Fisher Prize from the SSE

Dr. Matt Zuellig, a postdoctoral fellow in the Division of Evolutionary Ecology, has been awarded the 2019 R. A. Fisher Prize, which is awarded annually by the Society for the Study of Evolution for an outstanding Ph.D. dissertation paper published in an issue of the journal Evolution during a given calendar year. Matt’s paper “A two‐locus hybrid incompatibility is widespread, polymorphic, and active in natural populations of Mimulus” was published in Evolution in 2018. During his PhD research at the University of Georgia, Matt identified the genes that underlie a two-locus hybrid incompatibility between two species of monkeyflowers: Mimulus guttatus and M. nasutus. In this paper, he mapped the distribution and frequency of these alleles in natural populations, providing insight to how speciation loci are maintained in the wild despite ongoing gene flow.

New paper by students from the Evolutionary Ecology research practical

Students Michelle Gygax and Ana Rentsch recently published a paper in the Journal of Evolutionary Biology in which they report the results of a project they conducted under the supervision of Dr. Diana Rennison during the 2016 Evolutionary Ecology research practical. They found that threespine sticklebacks raised in ponds with a predator (cutthroat trout) exhibited more lateral barring (stripes) than threespine sticklebacks raised in ponds without the predator. An increase in the presence of vertical barring was correlated with an increase in water clarity and littoral habitat use. These data provide experimental evidence to support the hypothesis that vertical barring has evolved in sticklebacks due to selection by visual predators for cryptic coloration in vegetated habitats.

Dr. Diana Rennison awarded a Marie Curie Fellowship

Dr. Diana Rennison, a postdoctoral fellow in the Division of Evolutionary Ecology, has been awarded a Marie Curie Fellowship. In her project, Diana will address an outstanding question in evolution: are the genetic mechanisms that underlie adaptation to different environments predictable? Theoretical work suggests that pleiotropy - when a single gene influences multiple traits - might be a factor that constrains the types of genes that are used during adaptive evolution. Diana will test this long-standing theory using genomic data from sticklebacks that have repeatedly and independently adapted to divergent habitats. Her work will provide insights into the mechanisms that underlie the repeatability and therefore the predictability of evolutionary responses to environmental challenges such as climate change.

Genetic coupling of female traits and female preference facilitates speciation

How are associations between traits under divergent selection and traits that contribute to assortative mating maintained in the face of gene flow during ecological speciation? In a new paper in Current Biology, Catherine Peichel, Dolph Schluter (University of British Columbia) and colleagues answer this question using a classic model of ecological speciation, sympatric benthic-limnetic sticklebacks. To allow for recombination between loci underlying assortative mating and those under divergent ecological selection, they assessed the mate choice of benthic-limnetic stickleback F2 hybrid females for wild benthic or limnetic males under natural conditions in ponds. Remarkably, F2 females chose males with a similar body shape and size to their own. Furthermore, genetic loci associated with F2 female mate choice also predicted F2 female morphology. These data provide empirical evidence to support the long-standing theoretical prediction that genetic coupling between assortative mating and traits under divergent selection can facilitate speciation in the face of gene flow.

How repeatable is evolution?

Across the Northern hemisphere, sticklebacks have independently adapted to living in different habitats that are found in adjacent lakes and streams. But, do the lake and stream sticklebacks always evolve in the same way? In a new paper in Nature Ecology & Evolution, Katie Peichel and many colleagues including Yoel Stuart and Dan Bolnick (University of Texas) and Andrew Hendry (McGill University), found that the evolution of lake and stream sticklebacks from 16 watersheds on Vancouver Island, Canada is sometimes repeatable, but not always. They found that the repeatability of evolution could be explained both by the extent of ecological similarity across lakes or streams and by the extent of migration between the lakes and streams. This study sheds new light on the factors that might allow us to predict evolution.

GENETICS Editors' Choice Award

Our paper on the genetic basis of schooling behaviour was selected for the 2016 Editors' Choice Award in the journal GENETICS. This work was selected because it provides one of the first examples of a genetic change that underlies the evolution of vertebrate behavior in the wild.

Genetics of adaptation in sticklebacks

David Marques and Katie Peichel collaborated on a comprehensive review of the lessons learned about the genetic and molecular basis of phenotypic diversity using stickleback fish as a model system. These studies in sticklebacks have provided answers to long-standing questions about the effect sizes and genomic distribution of mutations involved in adaptation, the role of regulatory mutations in phenotypic evolution, and the genetic and molecular basis of repeated phenotypic evolution. This review was published in a special issue of Philosophical Transactions of the Royal Society on “Evo-devo in the genomics era, and the origins of morphological diversity”.

Chromosome evolution

Research on the contribution of changes in chromosome structure and number to evolutionary processes has recently undergone a renaissance. This has been catalyzed by detailed knowledge of the molecular mechanisms that underlie chromosome structure and function, as well as advances in genome sequencing. To bring together molecular and evolutionary biologists working on chromosome evolution, Katie Peichel organized a Presidential Symposium of the American Genetic Association on the topic: “Chromosome Evolution: Molecular Mechanisms and Evolutionary Consequences”. This conference also resulted in a special issue edited by Katie for the Journal of Heredity, which has just been published.

Genetics of behavioural evolution

Schooling is a fascinating behavior that has long drawn the attention of behavioral biologists, neurobiologists, computational biologists, evolutionary biologists, and now geneticists. In this study published in GENETICS, Anna Greenwood and colleagues in the Peichel group used a model school assay and transgenic approaches to show that natural variation in schooling behavior between two populations of threespine sticklebacks is caused by the gene Ectodysplasin. This work provides a rare example of a genetic change that underlies the evolution of vertebrate behavior in the wild.

New Head of Division Evolutionary Ecology

Prof Dr Catherine (Katie) Peichel is excited to join the IEE as a new Professor and Head of the Division Evolutionary Ecology as of August 1. Katie is a geneticist with interests in the genetic and genomic changes that underlie phenotypic evolution, including adaptation, sex chromosome evolution, behavior and speciation. Before joining the IEE, Katie led a research group at the Fred Hutchinson Cancer Research Center in Seattle and was an Affiliate Professor in the Department of Biology at the University of Washington.

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