Publications

@article{Muller2020,

title = {A single gene underlies the dynamic evolution of poplar sex determination},

author = {Niels A. Müller and Birgit Kersten and Ana P. Leite Montalvão and Niklas Mähler and Carolina Bernhardsson and Katharina Bräutigam and Zulema Carracedo Lorenzo and Hans Hoenicka and Vikash Kumar and Malte Mader and Birte Pakull and Kathryn M. Robinson and Maurizio Sabatti and Cristina Vettori and Pär K. Ingvarsson and Quentin Cronk and Nathaniel R. Street and Matthias Fladung},

url = {http://www.nature.com/articles/s41477-020-0672-9},

doi = {10.1038/s41477-020-0672-9},

issn = {2055-0278},

year  = {2020},

date = {2020-06-01},

journal = {Nature Plants},

pages = {1--8},

publisher = {Nature Publishing Group},

abstract = {Although hundreds of plant lineages have independently evolved dioecy (that is, separation of the sexes), the underlying genetic basis remains largely elusive1. Here we show that diverse poplar species carry partial duplicates of the ARABIDOPSIS RESPONSE REGULATOR 17 (ARR17) orthologue in the male-specific region of the Y chromosome. These duplicates give rise to small RNAs apparently causing male-specific DNA methylation and silencing of the ARR17 gene. CRISPR–Cas9-induced mutations demonstrate that ARR17 functions as a sex switch, triggering female development when on and male development when off. Despite repeated turnover events, including a transition from the XY system to a ZW system, the sex-specific regulation of ARR17 is conserved across the poplar genus and probably beyond. Our data reveal how a single-gene-based mechanism of dioecy can enable highly dynamic sex-linked regions and contribute to maintaining recombination and integrity of sex chromosomes. Populus has young sex chromosomes despite ancient dioecy. This study shows that the ARR17 gene functions as a sex switch, triggering female development when on and male development when off. This single-gene system enables dynamic evolution of poplar sex chromosomes.},

keywords = {evolution, Genomics, Natural variation in plants, Plant evolution, Plant genetics},

pubstate = {published},

tppubtype = {article}

}

@article{Libby1362757,

title = {Probabilistic Models for Predicting Mutational Routes to New Adaptive Phenotypes},

author = {Eric Libby and Peter A Lind},

doi = {10.21769/BioProtoc.3407},

year  = {2019},

date = {2019-01-01},

journal = {Bio-protocol},

volume = {9},

number = {20},

institution = {IceLab},

abstract = {Understanding the translation of genetic variation to phenotypic variation is a fundamental problem in genetics and evolutionary biology. The introduction of new genetic variation through mutation can lead to new adaptive phenotypes, but the complexity of the genotype-to-phenotype map makes it challenging to predict the phenotypic effects of mutation. Metabolic models, in conjunction with flux balance analysis, have been used to predict evolutionary optimality. These methods however rely on large scale models of metabolism, describe a limited set of phenotypes, and assume that selection for growth rate is the prime evolutionary driver. Here we describe a method for computing the relative likelihood that mutational change will translate into a phenotypic change between two molecular pathways. The interactions of molecular components in the pathways are modeled with ordinary differential equations. Unknown parameters are offset by probability distributions that describe the concentrations of molecular components, the reaction rates for different molecular processes, and the effects of mutations. Finally, the likelihood that mutations in a pathway will yield phenotypic change is estimated with stochastic simulations. One advantage of this method is that only basic knowledge of the interaction network underlying a phenotype is required. However, it can also incorporate available information about concentrations and reaction rates as well as mutational biases and mutational robustness of molecular components. The method estimates the relative probabilities that different pathways produce phenotypic change, which can be combined with fitness models to predict evolutionary outcomes.},

keywords = {Adaptation, evolution, Evolutionary forecasting, Genotype-to-phenotype map, Mathematical modeling, Mutation},

pubstate = {published},

tppubtype = {article}

}

@article{Nystedt2013,

title = {The Norway spruce genome sequence and conifer genome evolution},

author = {Björn Nystedt and Nathaniel R. Street and Anna Wetterbom and Andrea Zuccolo and Yao-Cheng Lin and Douglas G. Scofield and Francesco Vezzi and Nicolas Delhomme and Stefania Giacomello and Andrey Alexeyenko and Riccardo Vicedomini and Kristoffer Sahlin and Ellen Sherwood and Malin Elfstrand and Lydia Gramzow and Kristina Holmberg and Jimmie Hällman and Olivier Keech and Lisa Klasson and Maxim Koriabine and Melis Kucukoglu and Max Käller and Johannes Luthman and Fredrik Lysholm and Totte Niittylä and Åke Olson and Nemanja Rilakovic and Carol Ritland and Josep A. Rosselló and Juliana Sena and Thomas Svensson and Carlos Talavera-López and Günter Theißen and Hannele Tuominen and Kevin Vanneste and Zhi-Qiang Wu and Bo Zhang and Philipp Zerbe and Lars Arvestad and Rishikesh Bhalerao and Joerg Bohlmann and Jean Bousquet and Rosario Garcia Gil and Torgeir R. Hvidsten and Pieter Jong and John MacKay and Michele Morgante and Kermit Ritland and Björn Sundberg and Stacey Lee Thompson and Yves Van de Peer and Björn Andersson and Ove Nilsson and Pär K. Ingvarsson and Joakim Lundeberg and Stefan Jansson},

url = {http://www.nature.com/doifinder/10.1038/nature12211},

doi = {10.1038/nature12211},

issn = {0028-0836},

year  = {2013},

date = {2013-05-01},

journal = {Nature},

volume = {497},

number = {7451},

pages = {579--584},

abstract = {Conifers have dominated forests for more than 200 million years and are of huge ecological and economic importance. Here we present the draft assembly of the 20-gigabase genome of Norway spruce (Picea abies), the first available for any gymnosperm. The number of well-supported genes (28,354) is similar to the .100 times smaller genome of Arabidopsis thaliana, and there is no evidence of a recent whole-genome duplication in the gymnosperm lineage. Instead, the large genome size seems to result from the slow and steady accumulation of a diverse set of long-terminal repeat transposable elements, possibly owing to the lack of an efficient elimination mechanism. Comparative sequencing of Pinus sylvestris, Abies sibirica, Juniperus communis, Taxus baccata and Gnetum gnemon reveals that the transposable element diversity is shared among extant conifers. Expression of 24-nucleotide small RNAs, previously implicated in transposable element silencing, is tissue-specific and much lower than in other plants. We further identify numerous long (.10,000 base pairs) introns, gene-like fragments, uncharacterized long non-coding RNAs and short RNAs. This opens up new genomic avenues for conifer forestry and breeding. Gymnosperms are a group of land plants comprising the extant taxa, cycads, Ginkgo, gnetophytes and conifers. Gymnosperms first appeared more than 300 million years ago (Myr ago) 1 , well before the angiosperm lineage separated from the stem group of extant gymnosperms 2 . The major radiation of conifer families occurred 250–65 Myr ago 3 , and during their evolution the morphology of conifers has changed rela-tively little. There are approximately 630 conifer species, representing about 70 currently recognized genera, which dominate many terrestrial ecosystems, especially in the Northern Hemisphere. Conifers also dominated both before and after the major mass extinction events at the end of the Permian and Cretaceous periods, around 250 and 65 Myr ago, respectively. Conifers are of immense ecological and economic value; coniferous forests cover enormous areas in the Northern Hemi-sphere, and conifers are keystone species in many other ecosystems. Conifers contribute a large fraction of terrestrial photosynthesis and biomass, and the cultural and economic values of conifers are also para-mount; early civilizations used conifers for firewood, tools and artefacts and today several national economies depend on commodities produced from conifers. However, despite their abundance and importance, our understanding of conifer genomes is limited. Most conifers have 12 (2n 5 24) chromosomes, probably reflecting the ancestral karyotype 4},

keywords = {Conserved Sequence, Conserved Sequence: genetics, DNA, DNA Transposable Elements, DNA Transposable Elements: genetics, evolution, Gene Silencing, Genes, Genetic, Genetic: genetics, Genome, Genomics, Internet, Introns, Introns: genetics, Molecular, Phenotype, Picea, Picea: genetics, Plant, Plant: genetics, RNA, Sequence Analysis, Terminal Repeat Sequences, Terminal Repeat Sequences: genetics, transcription, Untranslated, Untranslated: genetics},

pubstate = {published},

tppubtype = {article}

}

@article{Libby2019,

title = {Shortsighted Evolution Constrains the Efficacy of Long-Term Bet Hedging},

author = {Eric Libby and William C. Ratcliff},

url = {https://www.journals.uchicago.edu/doi/abs/10.1086/701786},

doi = {10.1086/701786},

journal = {The American Naturalist},

volume = {0},

abstract = {To survive unpredictable environmental change, many organisms adopt bet-hedging strategies that are initially costly but provide a long-term fitness benefit. The temporal extent of these deferred fitness benefits determines whether bet-hedging organisms can survive long enough to realize them. In this article, we examine a model of microbial bet hedging in which there are two paths to extinction: unpredictable environmental change and demographic stochasticity. In temporally correlated environments, these drivers of extinction select for different switching strategies. Rapid phenotype switching ensures survival in the face of unpredictable environmental change, while slower-switching organisms become extinct. However, when both switching strategies are present in the same population, then demographic stochasticity—enforced by a limited population size—leads to extinction of the faster-switching organism. As a result, we find a novel form of evolutionary suicide whereby selection in a fluctuating environment can favor bet-hedging strategies that ultimately increase the risk of extinction. Population structures with multiple subpopulations and dispersal can reduce the risk of extinction from unpredictable environmental change and shift the balance so as to facilitate the evolution of slower-switching organisms.},

keywords = {evolution, extinction, Libby},

pubstate = {forthcoming},

tppubtype = {article}

}