@misc{12933, abstract = {Datasets of the publication "Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster".}, author = {Puixeu Sala, Gemma}, publisher = {Institute of Science and Technology Austria}, title = {{Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster}}, doi = {10.15479/AT:ISTA:12933}, year = {2023}, } @misc{12949, abstract = {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.}, author = {Barton, Nicholas H}, keywords = {Quantitative genetics, infinitesimal model}, publisher = {Institute of Science and Technology Austria}, title = {{The infinitesimal model with dominance}}, doi = {10.15479/AT:ISTA:12949}, year = {2023}, } @phdthesis{14058, abstract = {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.}, author = {Puixeu Sala, Gemma}, isbn = {978-3-99078-035-0}, issn = {2663-337X}, pages = {230}, publisher = {Institute of Science and Technology Austria}, title = {{The molecular basis of sexual dimorphism: Experimental and theoretical characterization of phenotypic, transcriptomic and genetic patterns of sex-specific adaptation}}, doi = {10.15479/at:ista:14058}, year = {2023}, } @article{14077, abstract = {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.}, author = {Puixeu Sala, Gemma and Macon, Ariana and Vicoso, Beatriz}, issn = {2160-1836}, journal = {G3: Genes, Genomes, Genetics}, keywords = {Genetics (clinical), Genetics, Molecular Biology}, number = {8}, publisher = {Oxford University Press}, title = {{Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster}}, doi = {10.1093/g3journal/jkad121}, volume = {13}, year = {2023}, } @article{14452, abstract = {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.}, author = {Barton, Nicholas H and Etheridge, Alison M. and Véber, Amandine}, issn = {1943-2631}, journal = {Genetics}, number = {2}, publisher = {Oxford University Press}, title = {{The infinitesimal model with dominance}}, doi = {10.1093/genetics/iyad133}, volume = {225}, year = {2023}, } @article{14552, abstract = {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.}, author = {Robinson, M. L. and Hahn, P. G. and Inouye, B. D. and Underwood, N. and Whitehead, S. R. and Abbott, K. C. and Bruna, E. M. and Cacho, N. I. and Dyer, L. A. and Abdala-Roberts, L. and Allen, W. J. and Andrade, J. F. and Angulo, D. F. and Anjos, D. and Anstett, D. N. and Bagchi, R. and Bagchi, S. and Barbosa, M. and Barrett, S. and Baskett, Carina and Ben-Simchon, E. and Bloodworth, K. J. and Bronstein, J. L. and Buckley, Y. M. and Burghardt, K. T. and Bustos-Segura, C. and Calixto, E. S. and Carvalho, R. L. and Castagneyrol, B. and Chiuffo, M. C. and Cinoğlu, D. and Cinto Mejía, E. and Cock, M. C. and Cogni, R. and Cope, O. L. and Cornelissen, T. and Cortez, D. R. and Crowder, D. W. and Dallstream, C. and Dáttilo, W. and Davis, J. K. and Dimarco, R. D. and Dole, H. E. and Egbon, I. N. and Eisenring, M. and Ejomah, A. and Elderd, B. D. and Endara, M. J. and Eubanks, M. D. and Everingham, S. E. and Farah, K. N. and Farias, R. P. and Fernandes, A. P. and Fernandes, G. W. and Ferrante, M. and Finn, A. and Florjancic, G. A. and Forister, M. L. and Fox, Q. N. and Frago, E. and França, F. M. and Getman-Pickering, A. S. and Getman-Pickering, Z. and Gianoli, E. and Gooden, B. and Gossner, M. M. and Greig, K. A. and Gripenberg, S. and Groenteman, R. and Grof-Tisza, P. and Haack, N. and Hahn, L. and Haq, S. M. and Helms, A. M. and Hennecke, J. and Hermann, S. L. and Holeski, L. M. and Holm, S. and Hutchinson, M. C. and Jackson, E. E. and Kagiya, S. and Kalske, A. and Kalwajtys, M. and Karban, R. and Kariyat, R. and Keasar, T. and Kersch-Becker, M. F. and Kharouba, H. M. and Kim, T. N. and Kimuyu, D. M. and Kluse, J. and Koerner, S. E. and Komatsu, K. J. and Krishnan, S. and Laihonen, M. and Lamelas-López, L. and Lascaleia, M. C. and Lecomte, N. and Lehn, C. R. and Li, X. and Lindroth, R. L. and Lopresti, E. F. and Losada, M. and Louthan, A. M. and Luizzi, V. J. and Lynch, S. C. and Lynn, J. S. and Lyon, N. J. and Maia, L. F. and Maia, R. A. and Mannall, T. L. and Martin, B. S. and Massad, T. J. and Mccall, A. C. and Mcgurrin, K. and Merwin, A. C. and Mijango-Ramos, Z. and Mills, C. H. and Moles, A. T. and Moore, C. M. and Moreira, X. and Morrison, C. R. and Moshobane, M. C. and Muola, A. and Nakadai, R. and Nakajima, K. and Novais, S. and Ogbebor, C. O. and Ohsaki, H. and Pan, V. S. and Pardikes, N. A. and Pareja, M. and Parthasarathy, N. and Pawar, R. R. and Paynter, Q. and Pearse, I. S. and Penczykowski, R. M. and Pepi, A. A. and Pereira, C. C. and Phartyal, S. S. and Piper, F. I. and Poveda, K. and Pringle, E. G. and Puy, J. and Quijano, T. and Quintero, C. and Rasmann, S. and Rosche, C. and Rosenheim, L. Y. and Rosenheim, J. A. and Runyon, J. B. and Sadeh, A. and Sakata, Y. and Salcido, D. M. and Salgado-Luarte, C. and Santos, B. A. and Sapir, Y. and Sasal, Y. and Sato, Y. and Sawant, M. and Schroeder, H. and Schumann, I. and Segoli, M. and Segre, H. and Shelef, O. and Shinohara, N. and Singh, R. P. and Smith, D. S. and Sobral, M. and Stotz, G. C. and Tack, A. J.M. and Tayal, M. and Tooker, J. F. and Torrico-Bazoberry, D. and Tougeron, K. and Trowbridge, A. M. and Utsumi, S. and Uyi, O. and Vaca-Uribe, J. L. and Valtonen, A. and Van Dijk, L. J.A. and Vandvik, V. and Villellas, J. and Waller, L. P. and Weber, M. G. and Yamawo, A. and Yim, S. and Zarnetske, P. L. and Zehr, L. N. and Zhong, Z. and Wetzel, W. C.}, issn = {1095-9203}, journal = {Science}, number = {6671}, pages = {679--683}, publisher = {AAAS}, title = {{Plant size, latitude, and phylogeny explain within-population variability in herbivory}}, doi = {10.1126/science.adh8830}, volume = {382}, year = {2023}, } @article{14556, abstract = {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.}, author = {Berdan, Emma L. and Barton, Nicholas H and Butlin, Roger and Charlesworth, Brian and Faria, Rui and Fragata, Inês and Gilbert, Kimberly J. and Jay, Paul and Kapun, Martin and Lotterhos, Katie E. and Mérot, Claire and Durmaz Mitchell, Esra and Pascual, Marta and Peichel, Catherine L. and Rafajlović, Marina and Westram, Anja M and Schaeffer, Stephen W. and Johannesson, Kerstin and Flatt, Thomas}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, number = {12}, publisher = {Wiley}, title = {{How chromosomal inversions reorient the evolutionary process}}, doi = {10.1111/jeb.14242}, volume = {36}, year = {2023}, } @misc{14579, abstract = {This is associated with our paper "Plant size, latitude, and phylogeny explain within-population variability in herbivory" published in Science. }, author = {Wetzel, William}, publisher = {Zenodo}, title = {{HerbVar-Network/HV-Large-Patterns-MS-public: v1.0.0}}, doi = {10.5281/ZENODO.8133117}, year = {2023}, } @phdthesis{14651, abstract = {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.}, author = {Arathoon, Louise S}, issn = {2663-337X}, pages = {96}, publisher = {Institute of Science and Technology Austria}, title = {{Investigating inbreeding depression and the self-incompatibility locus of Antirrhinum majus}}, doi = {10.15479/at:ista:14651}, year = {2023}, } @unpublished{14732, abstract = {Fragmented landscapes pose a significant threat to the persistence of species as they are highly susceptible to heightened risk of extinction due to the combined effects of genetic and demographic factors such as genetic drift and demographic stochasticity. This paper explores the intricate interplay between genetic load and extinction risk within metapopulations with a focus on understanding the impact of eco-evolutionary feedback mechanisms. We distinguish between two models of selection: soft selection, characterised by subpopulations maintaining carrying capacity despite load, and hard selection, where load can significantly affect population size. Within the soft selection framework, we investigate the impact of gene flow on genetic load at a single locus, while also considering the effect of selection strength and dominance coefficient. We subsequently build on this to examine how gene flow influences both population size and load under hard selection as well as identify critical thresholds for metapopulation persistence. Our analysis employs the diffusion, semi-deterministic and effective migration approximations. Our findings reveal that under soft selection, even modest levels of migration can significantly alleviate the burden of load. In sharp contrast, with hard selection, a much higher degree of gene flow is required to mitigate load and prevent the collapse of the metapopulation. Overall, this study sheds light into the crucial role migration plays in shaping the dynamics of genetic load and extinction risk in fragmented landscapes, offering valuable insights for conservation strategies and the preservation of diversity in a changing world.}, author = {Olusanya, Oluwafunmilola O and Khudiakova, Kseniia and Sachdeva, Himani}, booktitle = {bioRxiv}, title = {{Genetic load, eco-evolutionary feedback and extinction in a metapopulation}}, doi = {10.1101/2023.12.02.569702}, year = {2023}, } @article{14742, abstract = {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.}, author = {Lucek, Kay and Giménez, Mabel D. and Joron, Mathieu and Rafajlović, Marina and Searle, Jeremy B. and Walden, Nora and Westram, Anja M and Faria, Rui}, issn = {1943-0264}, journal = {Cold Spring Harbor Perspectives in Biology}, keywords = {General Biochemistry, Genetics and Molecular Biology}, number = {11}, publisher = {Cold Spring Harbor Laboratory Press}, title = {{The impact of chromosomal rearrangements in speciation: From micro- to macroevolution}}, doi = {10.1101/cshperspect.a041447}, volume = {15}, year = {2023}, } @article{14787, abstract = {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.}, author = {Stankowski, Sean and Chase, Madeline A. and McIntosh, Hanna and Streisfeld, Matthew A.}, issn = {1365-294X}, journal = {Molecular Ecology}, keywords = {Genetics, Ecology, Evolution, Behavior and Systematics}, number = {8}, pages = {2041--2054}, publisher = {Wiley}, title = {{Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone}}, doi = {10.1111/mec.16849}, volume = {32}, year = {2023}, } @misc{14812, abstract = {This repository contains the code and VCF files needed to conduct the analyses in our MS. Each folder contains a readMe document explaining the nature of each file and dataset and the results and analyses that they relate to. The same anlaysis code (but not VCF files) is also available at https://github.com/seanstankowski/Littorina_reproductive_mode}, author = {Stankowski, Sean}, publisher = {Zenodo}, title = {{Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails}}, doi = {10.5281/ZENODO.8318995}, year = {2023}, } @article{14833, abstract = {Understanding the factors that have shaped the current distributions and diversity of species is a central and longstanding aim of evolutionary biology. The recent inclusion of genomic data into phylogeographic studies has dramatically improved our understanding in organisms where evolutionary relationships have been challenging to infer. We used whole-genome sequences to study the phylogeography of the intertidal snail Littorina saxatilis, which has successfully colonized and diversified across a broad range of coastal environments in the Northern Hemisphere amid repeated cycles of glaciation. Building on past studies based on short DNA sequences, we used genome-wide data to provide a clearer picture of the relationships among samples spanning most of the species natural range. Our results confirm the trans-Atlantic colonization of North America from Europe, and have allowed us to identify rough locations of glacial refugia and to infer likely routes of colonization within Europe. We also investigated the signals in different datasets to account for the effects of genomic architecture and non-neutral evolution, which provides new insights about diversification of four ecotypes of L. saxatilis (the crab, wave, barnacle, and brackish ecotypes) at different spatial scales. Overall, we provide a much clearer picture of the biogeography of L. saxatilis, providing a foundation for more detailed phylogenomic and demographic studies.}, author = {Stankowski, Sean and Zagrodzka, Zuzanna B and Galindo, Juan and Montaño-Rendón, Mauricio and Faria, Rui and Mikhailova, Natalia and Blakeslee, April M H and Arnason, Einar and Broquet, Thomas and Morales, Hernán E and Grahame, John W and Westram, Anja M and Johannesson, Kerstin and Butlin, Roger K}, issn = {2752-938X}, journal = {Evolutionary Journal of the Linnean Society}, number = {1}, publisher = {Oxford University Press}, title = {{Whole-genome phylogeography of the intertidal snail Littorina saxatilis}}, doi = {10.1093/evolinnean/kzad002}, volume = {2}, year = {2023}, } @phdthesis{12800, abstract = {The evolutionary processes that brought about today’s plethora of living species and the many billions more ancient ones all underlie biology. Evolutionary pathways are neither directed nor deterministic, but rather an interplay between selection, migration, mutation, genetic drift and other environmental factors. Hybrid zones, as natural crossing experiments, offer a great opportunity to use cline analysis to deduce different evolutionary processes - for example, selection strength. Theoretical cline models, largely assuming uniform distribution of individuals, often lack the capability of incorporating population structure. Since in reality organisms mostly live in patchy distributions and their dispersal is hardly ever Gaussian, it is necessary to unravel the effect of these different elements of population structure on cline parameters and shape. In this thesis, I develop a simulation inspired by the A. majus hybrid zone of a single selected locus under frequency dependent selection. This simulation enables us to untangle the effects of different elements of population structure as for example a low-density center and long-range dispersal. This thesis is therefore a first step towards theoretically untangling the effects of different elements of population structure on cline parameters and shape. }, author = {Julseth, Mara}, issn = {2791-4585}, pages = {21}, publisher = {Institute of Science and Technology Austria}, title = {{The effect of local population structure on genetic variation at selected loci in the A. majus hybrid zone}}, doi = {10.15479/at:ista:12800}, year = {2023}, } @article{12159, abstract = {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.}, author = {Shipilina, Daria and Pal, Arka and Stankowski, Sean and Chan, Yingguang Frank and Barton, Nicholas H}, issn = {1365-294X}, journal = {Molecular Ecology}, keywords = {Genetics, Ecology, Evolution, Behavior and Systematics}, number = {6}, pages = {1441--1457}, publisher = {Wiley}, title = {{On the origin and structure of haplotype blocks}}, doi = {10.1111/mec.16793}, volume = {32}, year = {2023}, } @phdthesis{11128, abstract = {Although we often see studies focusing on simple or even discrete traits in studies of colouration, the variation of “appearance” phenotypes found in nature is often more complex, continuous and high-dimensional. Therefore, we developed automated methods suitable for large datasets of genomes and images, striving to account for their complex nature, while minimising human bias. We used these methods on a dataset of more than 20, 000 plant SNP genomes and corresponding fower images from a hybrid zone of two subspecies of Antirrhinum majus with distinctly coloured fowers to improve our understanding of the genetic nature of the fower colour in our study system. Firstly, we use the advantage of large numbers of genotyped plants to estimate the haplotypes in the main fower colour regulating region. We study colour- and geography-related characteristics of the estimated haplotypes and how they connect to their relatedness. We show discrepancies from the expected fower colour distributions given the genotype and identify particular haplotypes leading to unexpected phenotypes. We also confrm a signifcant defcit of the double recessive recombinant and quite surprisingly, we show that haplotypes of the most frequent parental type are much less variable than others. Secondly, we introduce our pipeline capable of processing tens of thousands of full fower images without human interaction and summarising each image into a set of informative scores. We show the compatibility of these machine-measured fower colour scores with the previously used manual scores and study impact of external efect on the resulting scores. Finally, we use the machine-measured fower colour scores to ft and examine a phenotype cline across the hybrid zone in Planoles using full fower images as opposed to discrete, manual scores and compare it with the genotypic cline.}, author = {Matejovicova, Lenka}, isbn = {978-3-99078-016-9}, issn = {2663-337X}, pages = {112}, publisher = {Institute of Science and Technology Austria}, title = {{Genetic basis of flower colour as a model for adaptive evolution}}, doi = {10.15479/at:ista:11128}, year = {2022}, } @misc{11321, abstract = {Here are the research data underlying the publication "Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus" Further information are summed up in the README document. }, author = {Surendranadh, Parvathy and Arathoon, Louise S and Baskett, Carina and Field, David and Pickup, Melinda and Barton, Nicholas H}, publisher = {Institute of Science and Technology Austria}, title = {{Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus}}, doi = {10.15479/at:ista:11321}, year = {2022}, } @article{11334, abstract = {Hybridization is a common evolutionary process with multiple possible outcomes. In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic hybrid species. However, it is unknown whether the generation of parthenogenetic hybrids is a rare outcome of frequent hybridization between sexual species within a genus or the typical outcome of rare hybridization events. Darevskia is a genus of rock lizards with both hybrid parthenogenetic and sexual species. Using capture sequencing, we estimate phylogenetic relationships and gene flow among the sexual species, to determine how introgressive hybridization relates to the origins of parthenogenetic hybrids. We find evidence for widespread hybridization with gene flow, both between recently diverged species and deep branches. Surprisingly, we find no signal of gene flow between parental species of the parthenogenetic hybrids, suggesting that the parental pairs were either reproductively or geographically isolated early in their divergence. The generation of parthenogenetic hybrids in Darevskia is, then, a rare outcome of the total occurrence of hybridization within the genus, but the typical outcome when specific species pairs hybridize. Our results question the conventional view that parthenogenetic lineages are generated by hybridization in a window of divergence. Instead, they suggest that some lineages possess specific properties that underpin successful parthenogenetic reproduction.}, author = {Freitas, Susana and Westram, Anja M and Schwander, Tanja and Arakelyan, Marine and Ilgaz, Çetin and Kumlutas, Yusuf and Harris, David James and Carretero, Miguel A. and Butlin, Roger K.}, issn = {1558-5646}, journal = {Evolution}, number = {5}, pages = {899--914}, publisher = {Wiley}, title = {{Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization}}, doi = {10.1111/evo.14462}, volume = {76}, year = {2022}, } @article{11411, abstract = {Many studies have quantified the distribution of heterozygosity and relatedness in natural populations, but few have examined the demographic processes driving these patterns. In this study, we take a novel approach by studying how population structure affects both pairwise identity and the distribution of heterozygosity in a natural population of the self-incompatible plant Antirrhinum majus. Excess variance in heterozygosity between individuals is due to identity disequilibrium, which reflects the variance in inbreeding between individuals; it is measured by the statistic g2. We calculated g2 together with FST and pairwise relatedness (Fij) using 91 SNPs in 22,353 individuals collected over 11 years. We find that pairwise Fij declines rapidly over short spatial scales, and the excess variance in heterozygosity between individuals reflects significant variation in inbreeding. Additionally, we detect an excess of individuals with around half the average heterozygosity, indicating either selfing or matings between close relatives. We use 2 types of simulation to ask whether variation in heterozygosity is consistent with fine-scale spatial population structure. First, by simulating offspring using parents drawn from a range of spatial scales, we show that the known pollen dispersal kernel explains g2. Second, we simulate a 1,000-generation pedigree using the known dispersal and spatial distribution and find that the resulting g2 is consistent with that observed from the field data. In contrast, a simulated population with uniform density underestimates g2, indicating that heterogeneous density promotes identity disequilibrium. Our study shows that heterogeneous density and leptokurtic dispersal can together explain the distribution of heterozygosity.}, author = {Surendranadh, Parvathy and Arathoon, Louise S and Baskett, Carina and Field, David and Pickup, Melinda and Barton, Nicholas H}, issn = {1943-2631}, journal = {Genetics}, number = {3}, publisher = {Oxford University Press}, title = {{Effects of fine-scale population structure on the distribution of heterozygosity in a long-term study of Antirrhinum majus}}, doi = {10.1093/genetics/iyac083}, volume = {221}, year = {2022}, }