TY - JOUR AB - Elaborate sexual signals are thought to have evolved and be maintained to serve as honest indicators of signaller quality. One measure of quality is health, which can be affected by parasite infection. Cnemaspis mysoriensis is a diurnal gecko that is often infested with ectoparasites in the wild, and males of this species express visual (coloured gular patches) and chemical (femoral gland secretions) traits that receivers could assess during social interactions. In this paper, we tested whether ectoparasites affect individual health, and whether signal quality is an indicator of ectoparasite levels. In wild lizards, we found that ectoparasite level was negatively correlated with body condition in both sexes. Moreover, some characteristics of both visual and chemical traits in males were strongly associated with ectoparasite levels. Specifically, males with higher ectoparasite levels had yellow gular patches with lower brightness and chroma, and chemical secretions with a lower proportion of aromatic compounds. We then determined whether ectoparasite levels in males influence female behaviour. Using sequential choice trials, wherein females were provided with either the visual or the chemical signals of wild-caught males that varied in ectoparasite level, we found that only chemical secretions evoked an elevated female response towards less parasitised males. Simultaneous choice trials in which females were exposed to the chemical secretions from males that varied in parasite level further confirmed a preference for males with lower parasites loads. Overall, we find that although health (body condition) or ectoparasite load can be honestly advertised through multiple modalities, the parasite-mediated female response is exclusively driven by chemical signals. AU - Pal, Arka AU - Joshi, Mihir AU - Thaker, Maria ID - 14850 IS - 1 JF - Journal of Experimental Biology KW - Insect Science KW - Molecular Biology KW - Animal Science and Zoology KW - Aquatic Science KW - Physiology KW - Ecology KW - Evolution KW - Behavior and Systematics SN - 1477-9145 TI - Too much information? Males convey parasite levels using more signal modalities than females utilise VL - 227 ER - TY - THES AB - In nature, different species find their niche in a range of environments, each with its unique characteristics. While some thrive in uniform (homogeneous) landscapes where environmental conditions stay relatively consistent across space, others traverse the complexities of spatially heterogeneous terrains. Comprehending how species are distributed and how they interact within these landscapes holds the key to gaining insights into their evolutionary dynamics while also informing conservation and management strategies. For species inhabiting heterogeneous landscapes, when the rate of dispersal is low compared to spatial fluctuations in selection pressure, localized adaptations may emerge. Such adaptation in response to varying selection strengths plays an important role in the persistence of populations in our rapidly changing world. Hence, species in nature are continuously in a struggle to adapt to local environmental conditions, to ensure their continued survival. Natural populations can often adapt in time scales short enough for evolutionary changes to influence ecological dynamics and vice versa, thereby creating a feedback between evolution and demography. The analysis of this feedback and the relative contributions of gene flow, demography, drift, and natural selection to genetic variation and differentiation has remained a recurring theme in evolutionary biology. Nevertheless, the effective role of these forces in maintaining variation and shaping patterns of diversity is not fully understood. Even in homogeneous environments devoid of local adaptations, such understanding remains elusive. Understanding this feedback is crucial, for example in determining the conditions under which extinction risk can be mitigated in peripheral populations subject to deleterious mutation accumulation at the edges of species’ ranges as well as in highly fragmented populations. In this thesis we explore both uniform and spatially heterogeneous metapopulations, investigating and providing theoretical insights into the dynamics of local adaptation in the latter and examining the dynamics of load and extinction as well as the impact of joint ecological and evolutionary (eco-evolutionary) dynamics in the former. The thesis is divided into 5 chapters. Chapter 1 provides a general introduction into the subject matter, clarifying concepts and ideas used throughout the thesis. In chapter 2, we explore how fast a species distributed across a heterogeneous landscape adapts to changing conditions marked by alterations in carrying capacity, selection pressure, and migration rate. In chapter 3, we investigate how migration selection and drift influences adaptation and the maintenance of variation in a metapopulation with three habitats, an extension of previous models of adaptation in two habitats. We further develop analytical approximations for the critical threshold required for polymorphism to persist. The focus of chapter 4 of the thesis is on understanding the interplay between ecology and evolution as coupled processes. We investigate how eco-evolutionary feedback between migration, selection, drift, and demography influences eco-evolutionary outcomes in marginal populations subject to deleterious mutation accumulation. Using simulations as well as theoretical approximations of the coupled dynamics of population size and allele frequency, we analyze how gene flow from a large mainland source influences genetic load and population size on an island (i.e., in a marginal population) under genetically realistic assumptions. Analyses of this sort are important because small isolated populations, are repeatedly affected by complex interactions between ecological and evolutionary processes, which can lead to their death. Understanding these interactions can therefore provide an insight into the conditions under which extinction risk can be mitigated in peripheral populations thus, contributing to conservation and restoration efforts. Chapter 5 extends the analysis in chapter 4 to consider the dynamics of load (due to deleterious mutation accumulation) and extinction risk in a metapopulation. We explore the role of gene flow, selection, and dominance on load and extinction risk and further pinpoint critical thresholds required for metapopulation persistence. Overall this research contributes to our understanding of ecological and evolutionary mechanisms that shape species’ persistence in fragmented landscapes, a crucial foundation for successful conservation efforts and biodiversity management. AU - Olusanya, Oluwafunmilola O ID - 14711 SN - 2663 - 337X TI - Local adaptation, genetic load and extinction in metapopulations ER - TY - JOUR AB - Key innovations are fundamental to biological diversification, but their genetic basis is poorly understood. A recent transition from egg-laying to live-bearing in marine snails (Littorina spp.) provides the opportunity to study the genetic architecture of an innovation that has evolved repeatedly across animals. Individuals do not cluster by reproductive mode in a genome-wide phylogeny, but local genealogical analysis revealed numerous small genomic regions where all live-bearers carry the same core haplotype. Candidate regions show evidence for live-bearer–specific positive selection and are enriched for genes that are differentially expressed between egg-laying and live-bearing reproductive systems. Ages of selective sweeps suggest that live-bearer–specific alleles accumulated over more than 200,000 generations. Our results suggest that new functions evolve through the recruitment of many alleles rather than in a single evolutionary step. AU - Stankowski, Sean AU - Zagrodzka, Zuzanna B. AU - Garlovsky, Martin D. AU - Pal, Arka AU - Shipilina, Daria AU - Garcia Castillo, Diego Fernando AU - Lifchitz, Hila AU - Le Moan, Alan AU - Leder, Erica AU - Reeve, James AU - Johannesson, Kerstin AU - Westram, Anja M AU - Butlin, Roger K. ID - 14796 IS - 6678 JF - Science TI - The genetic basis of a recent transition to live-bearing in marine snails VL - 383 ER - TY - THES AB - This thesis consists of four distinct pieces of work within theoretical biology, with two themes in common: the concept of optimization in biological systems, and the use of information-theoretic tools to quantify biological stochasticity and statistical uncertainty. Chapter 2 develops a statistical framework for studying biological systems which we believe to be optimized for a particular utility function, such as retinal neurons conveying information about visual stimuli. We formalize such beliefs as maximum-entropy Bayesian priors, constrained by the expected utility. We explore how such priors aid inference of system parameters with limited data and enable optimality hypothesis testing: is the utility higher than by chance? Chapter 3 examines the ultimate biological optimization process: evolution by natural selection. As some individuals survive and reproduce more successfully than others, populations evolve towards fitter genotypes and phenotypes. We formalize this as accumulation of genetic information, and use population genetics theory to study how much such information can be accumulated per generation and maintained in the face of random mutation and genetic drift. We identify the population size and fitness variance as the key quantities that control information accumulation and maintenance. Chapter 4 reuses the concept of genetic information from Chapter 3, but from a different perspective: we ask how much genetic information organisms actually need, in particular in the context of gene regulation. For example, how much information is needed to bind transcription factors at correct locations within the genome? Population genetics provides us with a refined answer: with an increasing population size, populations achieve higher fitness by maintaining more genetic information. Moreover, regulatory parameters experience selection pressure to optimize the fitness-information trade-off, i.e. minimize the information needed for a given fitness. This provides an evolutionary derivation of the optimization priors introduced in Chapter 2. Chapter 5 proves an upper bound on mutual information between a signal and a communication channel output (such as neural activity). Mutual information is an important utility measure for biological systems, but its practical use can be difficult due to the large dimensionality of many biological channels. Sometimes, a lower bound on mutual information is computed by replacing the high-dimensional channel outputs with decodes (signal estimates). Our result provides a corresponding upper bound, provided that the decodes are the maximum posterior estimates of the signal. AU - Hledik, Michal ID - 15020 KW - Theoretical biology KW - Optimality KW - Evolution KW - Information SN - 2663 - 337X TI - Genetic information and biological optimization ER - TY - JOUR AB - Speciation is a key evolutionary process that is not yet fully understood. Combining population genomic and ecological data from multiple diverging pairs of marine snails (Littorina) supports the search for speciation mechanisms. Placing pairs on a one-dimensional speciation continuum, from undifferentiated populations to species, obscured the complexity of speciation. Adding multiple axes helped to describe either speciation routes or reproductive isolation in the snails. Divergent ecological selection repeatedly generated barriers between ecotypes, but appeared less important in completing speciation while genetic incompatibilities played a key role. Chromosomal inversions contributed to genomic barriers, but with variable impact. A multidimensional (hypercube) approach supported framing of questions and identification of knowledge gaps and can be useful to understand speciation in many other systems. AU - Johannesson, Kerstin AU - Faria, Rui AU - Le Moan, Alan AU - Rafajlović, Marina AU - Westram, Anja M AU - Butlin, Roger K. AU - Stankowski, Sean ID - 15099 JF - Trends in Genetics SN - 0168-9525 TI - Diverse pathways to speciation revealed by marine snails ER - TY - JOUR AB - Understanding population divergence that eventually leads to speciation is essential for evolutionary biology. High species diversity in the sea was regarded as a paradox when strict allopatry was considered necessary for most speciation events because geographical barriers seemed largely absent in the sea, and many marine species have high dispersal capacities. Combining genome-wide data with demographic modelling to infer the demographic history of divergence has introduced new ways to address this classical issue. These models assume an ancestral population that splits into two subpopulations diverging according to different scenarios that allow tests for periods of gene flow. Models can also test for heterogeneities in population sizes and migration rates along the genome to account, respectively, for background selection and selection against introgressed ancestry. To investigate how barriers to gene flow arise in the sea, we compiled studies modelling the demographic history of divergence in marine organisms and extracted preferred demographic scenarios together with estimates of demographic parameters. These studies show that geographical barriers to gene flow do exist in the sea but that divergence can also occur without strict isolation. Heterogeneity of gene flow was detected in most population pairs suggesting the predominance of semipermeable barriers during divergence. We found a weak positive relationship between the fraction of the genome experiencing reduced gene flow and levels of genome-wide differentiation. Furthermore, we found that the upper bound of the ‘grey zone of speciation’ for our dataset extended beyond that found before, implying that gene flow between diverging taxa is possible at higher levels of divergence than previously thought. Finally, we list recommendations for further strengthening the use of demographic modelling in speciation research. These include a more balanced representation of taxa, more consistent and comprehensive modelling, clear reporting of results and simulation studies to rule out nonbiological explanations for general results. AU - De Jode, Aurélien AU - Le Moan, Alan AU - Johannesson, Kerstin AU - Faria, Rui AU - Stankowski, Sean AU - Westram, Anja M AU - Butlin, Roger K. AU - Rafajlović, Marina AU - Fraisse, Christelle ID - 11479 IS - 2 JF - Evolutionary Applications TI - Ten years of demographic modelling of divergence and speciation in the sea VL - 16 ER - TY - JOUR AB - The concept of a “speciation continuum” has gained popularity in recent decades. It emphasizes speciation as a continuous process that may be studied by comparing contemporary population pairs that show differing levels of divergence. In their recent perspective article in Evolution, Stankowski and Ravinet provided a valuable service by formally defining the speciation continuum as a continuum of reproductive isolation, based on opinions gathered from a survey of speciation researchers. While we agree that the speciation continuum has been a useful concept to advance the understanding of the speciation process, some intrinsic limitations exist. Here, we advocate for a multivariate extension, the speciation hypercube, first proposed by Dieckmann et al. in 2004, but rarely used since. We extend the idea of the speciation cube and suggest it has strong conceptual and practical advantages over a one-dimensional model. We illustrate how the speciation hypercube can be used to visualize and compare different speciation trajectories, providing new insights into the processes and mechanisms of speciation. A key strength of the speciation hypercube is that it provides a unifying framework for speciation research, as it allows questions from apparently disparate subfields to be addressed in a single conceptual model. AU - Bolnick, Daniel I. AU - Hund, Amanda K. AU - Nosil, Patrik AU - Peng, Foen AU - Ravinet, Mark AU - Stankowski, Sean AU - Subramanian, Swapna AU - Wolf, Jochen B.W. AU - Yukilevich, Roman ID - 12514 IS - 1 JF - Evolution: International journal of organic evolution TI - A multivariate view of the speciation continuum VL - 77 ER - TY - JOUR AB - The term “haplotype block” is commonly used in the developing field of haplotype-based inference methods. We argue that the term should be defined based on the structure of the Ancestral Recombination Graph (ARG), which contains complete information on the ancestry of a sample. We use simulated examples to demonstrate key features of the relationship between haplotype blocks and ancestral structure, emphasizing the stochasticity of the processes that generate them. Even the simplest cases of neutrality or of a “hard” selective sweep produce a rich structure, often missed by commonly used statistics. We highlight a number of novel methods for inferring haplotype structure, based on the full ARG, or on a sequence of trees, and illustrate how they can be used to define haplotype blocks using an empirical data set. While the advent of new, computationally efficient methods makes it possible to apply these concepts broadly, they (and additional new methods) could benefit from adding features to explore haplotype blocks, as we define them. Understanding and applying the concept of the haplotype block will be essential to fully exploit long and linked-read sequencing technologies. AU - Shipilina, Daria AU - Pal, Arka AU - Stankowski, Sean AU - Chan, Yingguang Frank AU - Barton, Nicholas H ID - 12159 IS - 6 JF - Molecular Ecology KW - Genetics KW - Ecology KW - Evolution KW - Behavior and Systematics SN - 0962-1083 TI - On the origin and structure of haplotype blocks VL - 32 ER - TY - JOUR AB - The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and an environmental component, and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the parental traits. In previous work, we showed that when trait values are determined by the sum of a large number of additive Mendelian factors, each of small effect, one can justify the infinitesimal model as a limit of Mendelian inheritance. In this paper, we show that this result extends to include dominance. We define the model in terms of classical quantities of quantitative genetics, before justifying it as a limit of Mendelian inheritance as the number, M, of underlying loci tends to infinity. As in the additive case, the multivariate normal distribution of trait values across the pedigree can be expressed in terms of variance components in an ancestral population and probabilities of identity by descent determined by the pedigree. Now, with just first-order dominance effects, we require two-, three-, and four-way identities. We also show that, even if we condition on parental trait values, the “shared” and “residual” components of trait values within each family will be asymptotically normally distributed as the number of loci tends to infinity, with an error of order 1/M−−√⁠. We illustrate our results with some numerical examples. AU - Barton, Nicholas H AU - Etheridge, Alison M. AU - Véber, Amandine ID - 14452 IS - 2 JF - Genetics SN - 0016-6731 TI - The infinitesimal model with dominance VL - 225 ER - TY - DATA AB - The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and a non-genetic (environmental) component and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the trait values of the parents. Although the trait distribution across the whole population can be far from normal, the trait distributions within families are normally distributed with a variance-covariance matrix that is determined entirely by that in the ancestral population and the probabilities of identity determined by the pedigree. Moreover, conditioning on some of the trait values within the pedigree has predictable effects on the mean and variance within and between families. In previous work, Barton et al. (2017), we showed that when trait values are determined by the sum of a large number of Mendelian factors, each of small effect, one can justify the infinitesimal model as limit of Mendelian inheritance. It was also shown that under some forms of epistasis, trait values within a family are still normally distributed. AU - Barton, Nicholas H ID - 12949 KW - Quantitative genetics KW - infinitesimal model TI - The infinitesimal model with dominance ER - 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 -