TY - JOUR AB - Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach. AU - Berdan, Emma L. AU - Barton, Nicholas H AU - Butlin, Roger AU - Charlesworth, Brian AU - Faria, Rui AU - Fragata, Inês AU - Gilbert, Kimberly J. AU - Jay, Paul AU - Kapun, Martin AU - Lotterhos, Katie E. AU - Mérot, Claire AU - Durmaz Mitchell, Esra AU - Pascual, Marta AU - Peichel, Catherine L. AU - Rafajlović, Marina AU - Westram, Anja M AU - Schaeffer, Stephen W. AU - Johannesson, Kerstin AU - Flatt, Thomas ID - 14556 JF - Journal of Evolutionary Biology SN - 1010-061X TI - How chromosomal inversions reorient the evolutionary process ER - TY - JOUR AB - Interactions between plants and herbivores are central in most ecosystems, but their strength is highly variable. The amount of variability within a system is thought to influence most aspects of plant-herbivore biology, from ecological stability to plant defense evolution. Our understanding of what influences variability, however, is limited by sparse data. We collected standardized surveys of herbivory for 503 plant species at 790 sites across 116° of latitude. With these data, we show that within-population variability in herbivory increases with latitude, decreases with plant size, and is phylogenetically structured. Differences in the magnitude of variability are thus central to how plant-herbivore biology varies across macroscale gradients. We argue that increased focus on interaction variability will advance understanding of patterns of life on Earth. AU - Robinson, M. L. AU - Hahn, P. G. AU - Inouye, B. D. AU - Underwood, N. AU - Whitehead, S. R. AU - Abbott, K. C. AU - Bruna, E. M. AU - Cacho, N. I. AU - Dyer, L. A. AU - Abdala-Roberts, L. AU - Allen, W. J. AU - Andrade, J. F. AU - Angulo, D. F. AU - Anjos, D. AU - Anstett, D. N. AU - Bagchi, R. AU - Bagchi, S. AU - Barbosa, M. AU - Barrett, S. AU - Baskett, Carina AU - Ben-Simchon, E. AU - Bloodworth, K. J. AU - Bronstein, J. L. AU - Buckley, Y. M. AU - Burghardt, K. T. AU - Bustos-Segura, C. AU - Calixto, E. S. AU - Carvalho, R. L. AU - Castagneyrol, B. AU - Chiuffo, M. C. AU - Cinoğlu, D. AU - Cinto Mejía, E. AU - Cock, M. C. AU - Cogni, R. AU - Cope, O. L. AU - Cornelissen, T. AU - Cortez, D. R. AU - Crowder, D. W. AU - Dallstream, C. AU - Dáttilo, W. AU - Davis, J. K. AU - Dimarco, R. D. AU - Dole, H. E. AU - Egbon, I. N. AU - Eisenring, M. AU - Ejomah, A. AU - Elderd, B. D. AU - Endara, M. J. AU - Eubanks, M. D. AU - Everingham, S. E. AU - Farah, K. N. AU - Farias, R. P. AU - Fernandes, A. P. AU - Fernandes, G. W. AU - Ferrante, M. AU - Finn, A. AU - Florjancic, G. A. AU - Forister, M. L. AU - Fox, Q. N. AU - Frago, E. AU - França, F. M. AU - Getman-Pickering, A. S. AU - Getman-Pickering, Z. AU - Gianoli, E. AU - Gooden, B. AU - Gossner, M. M. AU - Greig, K. A. AU - Gripenberg, S. AU - Groenteman, R. AU - Grof-Tisza, P. AU - Haack, N. AU - Hahn, L. AU - Haq, S. M. AU - Helms, A. M. AU - Hennecke, J. AU - Hermann, S. L. AU - Holeski, L. M. AU - Holm, S. AU - Hutchinson, M. C. AU - Jackson, E. E. AU - Kagiya, S. AU - Kalske, A. AU - Kalwajtys, M. AU - Karban, R. AU - Kariyat, R. AU - Keasar, T. AU - Kersch-Becker, M. F. AU - Kharouba, H. M. AU - Kim, T. N. AU - Kimuyu, D. M. AU - Kluse, J. AU - Koerner, S. E. AU - Komatsu, K. J. AU - Krishnan, S. AU - Laihonen, M. AU - Lamelas-López, L. AU - Lascaleia, M. C. AU - Lecomte, N. AU - Lehn, C. R. AU - Li, X. AU - Lindroth, R. L. AU - Lopresti, E. F. AU - Losada, M. AU - Louthan, A. M. AU - Luizzi, V. J. AU - Lynch, S. C. AU - Lynn, J. S. AU - Lyon, N. J. AU - Maia, L. F. AU - Maia, R. A. AU - Mannall, T. L. AU - Martin, B. S. AU - Massad, T. J. AU - Mccall, A. C. AU - Mcgurrin, K. AU - Merwin, A. C. AU - Mijango-Ramos, Z. AU - Mills, C. H. AU - Moles, A. T. AU - Moore, C. M. AU - Moreira, X. AU - Morrison, C. R. AU - Moshobane, M. C. AU - Muola, A. AU - Nakadai, R. AU - Nakajima, K. AU - Novais, S. AU - Ogbebor, C. O. AU - Ohsaki, H. AU - Pan, V. S. AU - Pardikes, N. A. AU - Pareja, M. AU - Parthasarathy, N. AU - Pawar, R. R. AU - Paynter, Q. AU - Pearse, I. S. AU - Penczykowski, R. M. AU - Pepi, A. A. AU - Pereira, C. C. AU - Phartyal, S. S. AU - Piper, F. I. AU - Poveda, K. AU - Pringle, E. G. AU - Puy, J. AU - Quijano, T. AU - Quintero, C. AU - Rasmann, S. AU - Rosche, C. AU - Rosenheim, L. Y. AU - Rosenheim, J. A. AU - Runyon, J. B. AU - Sadeh, A. AU - Sakata, Y. AU - Salcido, D. M. AU - Salgado-Luarte, C. AU - Santos, B. A. AU - Sapir, Y. AU - Sasal, Y. AU - Sato, Y. AU - Sawant, M. AU - Schroeder, H. AU - Schumann, I. AU - Segoli, M. AU - Segre, H. AU - Shelef, O. AU - Shinohara, N. AU - Singh, R. P. AU - Smith, D. S. AU - Sobral, M. AU - Stotz, G. C. AU - Tack, A. J.M. AU - Tayal, M. AU - Tooker, J. F. AU - Torrico-Bazoberry, D. AU - Tougeron, K. AU - Trowbridge, A. M. AU - Utsumi, S. AU - Uyi, O. AU - Vaca-Uribe, J. L. AU - Valtonen, A. AU - Van Dijk, L. J.A. AU - Vandvik, V. AU - Villellas, J. AU - Waller, L. P. AU - Weber, M. G. AU - Yamawo, A. AU - Yim, S. AU - Zarnetske, P. L. AU - Zehr, L. N. AU - Zhong, Z. AU - Wetzel, W. C. ID - 14552 IS - 6671 JF - Science TI - Plant size, latitude, and phylogeny explain within-population variability in herbivory VL - 382 ER - TY - GEN AB - This is associated with our paper "Plant size, latitude, and phylogeny explain within-population variability in herbivory" published in Science. AU - Wetzel, William ID - 14579 TI - HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0 ER - TY - THES AB - Females and males across species are subject to divergent selective pressures arising from di↵erent reproductive interests and ecological niches. This often translates into a intricate array of sex-specific natural and sexual selection on traits that have a shared genetic basis between both sexes, causing a genetic sexual conflict. The resolution of this conflict mostly relies on the evolution of sex-specific expression of the shared genes, leading to phenotypic sexual dimorphism. Such sex-specific gene expression is thought to evolve via modifications of the genetic networks ultimately linked to sex-determining transcription factors. Although much empirical and theoretical evidence supports this standard picture of the molecular basis of sexual conflict resolution, there still are a few open questions regarding the complex array of selective forces driving phenotypic di↵erentiation between the sexes, as well as the molecular mechanisms underlying sexspecific adaptation. I address some of these open questions in my PhD thesis. First, how do patterns of phenotypic sexual dimorphism vary within populations, as a response to the temporal and spatial changes in sex-specific selective forces? To tackle this question, I analyze the patterns of sex-specific phenotypic variation along three life stages and across populations spanning the whole geographical range of Rumex hastatulus, a wind-pollinated angiosperm, in the first Chapter of the thesis. Second, how do gene expression patterns lead to phenotypic dimorphism, and what are the molecular mechanisms underlying the observed transcriptomic variation? I address this question by examining the sex- and tissue-specific expression variation in newly-generated datasets of sex-specific expression in heads and gonads of Drosophila melanogaster. I additionally used two complementary approaches for the study of the genetic basis of sex di↵erences in gene expression in the second and third Chapters of the thesis. Third, how does intersex correlation, thought to be one of the main aspects constraining the ability for the two sexes to decouple, interact with the evolution of sexual dimorphism? I develop models of sex-specific stabilizing selection, mutation and drift to formalize common intuition regarding the patterns of covariation between intersex correlation and sexual dimorphism in the fourth Chapter of the thesis. Alltogether, the work described in this PhD thesis provides useful insights into the links between genetic, transcriptomic and phenotypic layers of sex-specific variation, and contributes to our general understanding of the dynamics of sexual dimorphism evolution. AU - Puixeu Sala, Gemma ID - 14058 SN - 2663-337X TI - The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation ER - TY - JOUR AB - The regulatory architecture of gene expression is known to differ substantially between sexes in Drosophila, but most studies performed so far used whole-body data and only single crosses, which may have limited their scope to detect patterns that are robust across tissues and biological replicates. Here, we use allele-specific gene expression of parental and reciprocal hybrid crosses between 6 Drosophila melanogaster inbred lines to quantify cis- and trans-regulatory variation in heads and gonads of both sexes separately across 3 replicate crosses. Our results suggest that female and male heads, as well as ovaries, have a similar regulatory architecture. On the other hand, testes display more and substantially different cis-regulatory effects, suggesting that sex differences in the regulatory architecture that have been previously observed may largely derive from testis-specific effects. We also examine the difference in cis-regulatory variation of genes across different levels of sex bias in gonads and heads. Consistent with the idea that intersex correlations constrain expression and can lead to sexual antagonism, we find more cis variation in unbiased and moderately biased genes in heads. In ovaries, reduced cis variation is observed for male-biased genes, suggesting that cis variants acting on these genes in males do not lead to changes in ovary expression. Finally, we examine the dominance patterns of gene expression and find that sex- and tissue-specific patterns of inheritance as well as trans-regulatory variation are highly variable across biological crosses, although these were performed in highly controlled experimental conditions. This highlights the importance of using various genetic backgrounds to infer generalizable patterns. AU - Puixeu Sala, Gemma AU - Macon, Ariana AU - Vicoso, Beatriz ID - 14077 IS - 8 JF - G3: Genes, Genomes, Genetics KW - Genetics (clinical) KW - Genetics KW - Molecular Biology SN - 2160-1836 TI - Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster VL - 13 ER - TY - DATA AB - Datasets of the publication "Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster". AU - Puixeu Sala, Gemma ID - 12933 TI - Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster ER - TY - JOUR AB - Inversions are thought to play a key role in adaptation and speciation, suppressing recombination between diverging populations. Genes influencing adaptive traits cluster in inversions, and changes in inversion frequencies are associated with environmental differences. However, in many organisms, it is unclear if inversions are geographically and taxonomically widespread. The intertidal snail, Littorina saxatilis, is one such example. Strong associations between putative polymorphic inversions and phenotypic differences have been demonstrated between two ecotypes of L. saxatilis in Sweden and inferred elsewhere, but no direct evidence for inversion polymorphism currently exists across the species range. Using whole genome data from 107 snails, most inversion polymorphisms were found to be widespread across the species range. The frequencies of some inversion arrangements were significantly different among ecotypes, suggesting a parallel adaptive role. Many inversions were also polymorphic in the sister species, L. arcana, hinting at an ancient origin. AU - Reeve, James AU - Butlin, Roger K. AU - Koch, Eva L. AU - Stankowski, Sean AU - Faria, Rui ID - 14463 JF - Molecular Ecology SN - 0962-1083 TI - Chromosomal inversion polymorphisms are widespread across the species ranges of rough periwinkles (Littorina saxatilis and L. arcana) ER - TY - THES AB - For self-incompatibility (SI) to be stable in a population, theory predicts that sufficient inbreeding depression (ID) is required: the fitness of offspring from self-mated individuals must be low enough to prevent the spread of self-compatibility (SC). Reviews of natural plant populations have supported this theory, with SI species generally showing high levels of ID. However, there is thought to be an under-sampling of self-incompatible taxa in the current literature. In this thesis, I study inbreeding depression in the SI plant species Antirrhinum majus using both greenhouse crosses and a large collected field dataset. Additionally, the gametophytic S-locus of A. majus is highly heterozygous and polymorphic, thus making assembly and discovery of S-alleles very difficult. Here, 206 new alleles of the male component SLFs are presented, along with a phylogeny showing the high conservation with alleles from another Antirrhinum species. Lastly, selected sites within the protein structure of SLFs are investigated, with one site in particular highlighted as potentially being involved in the SI recognition mechanism. AU - Arathoon, Louise S ID - 14651 SN - 2663 - 337X TI - Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus ER - TY - JOUR AB - Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics. While an important role for CRs in speciation has been suggested, evidence primarily stems from theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon pairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at a macroevolutionary level has been supported by associations between species diversity and rates of evolution of CRs across phylogenies, these findings are limited to a restricted range of CRs and taxa. Now that more broadly applicable and precise CR detection approaches have become available, we address the challenges in filling some of the conceptual and empirical gaps between micro- and macroevolutionary studies on the role of CRs in speciation. We synthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life. AU - Lucek, Kay AU - Giménez, Mabel D. AU - Joron, Mathieu AU - Rafajlović, Marina AU - Searle, Jeremy B. AU - Walden, Nora AU - Westram, Anja M AU - Faria, Rui ID - 14742 IS - 11 JF - Cold Spring Harbor Perspectives in Biology KW - General Biochemistry KW - Genetics and Molecular Biology SN - 1943-0264 TI - The impact of chromosomal rearrangements in speciation: From micro- to macroevolution VL - 15 ER - TY - JOUR AB - Understanding the phenotypic and genetic architecture of reproductive isolation is a long‐standing goal of speciation research. In several systems, large‐effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine “top‐down” and “bottom‐up” approaches with demographic modelling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to gene flow between two divergent red‐ and yellow‐flowered ecotypes ofMimulus aurantiacus. Several candidate isolating traits and anonymous single nucleotide polymorphism loci under divergent selection have been identified, but their genomic positions remain unknown. Here, we report findings from demographic analyses that indicate this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted by widespread barrier loci across the genome. Using a novel, geographic cline‐based genome scan, we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few “islands of speciation.” Quantitative trait locus (QTL) mapping reveals that most floral traits are highly polygenic, with little evidence that QTL colocalize, indicating that most traits are genetically independent. Finally, we find little evidence that QTL and candidate barrier loci overlap, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow other than pollinator isolation may play an important role in this system. AU - Stankowski, Sean AU - Chase, Madeline A. AU - McIntosh, Hanna AU - Streisfeld, Matthew A. ID - 14787 IS - 8 JF - Molecular Ecology KW - Genetics KW - Ecology KW - Evolution KW - Behavior and Systematics SN - 0962-1083 TI - Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone VL - 32 ER -