@misc{18712, abstract = {This file contains the code associated with the manuscript 'Effect of assortative mating and sexual selection on polygenic barriers to gene flow'. }, author = {Surendranadh, Parvathy and Sachdeva, Himani}, publisher = {Institute of Science and Technology Austria}, title = {{Mathematica notebook and Fortran code for 'Effect of assortative mating and sexual selection on polygenic barriers to gene flow'}}, doi = {10.15479/AT:ISTA:17344}, year = {2025}, } @article{19876, abstract = {Assortative mating and sexual selection are widespread in nature and can play an important role in speciation by facilitating the buildup and maintenance of reproductive isolation (RI). However, their contribution to genome-wide suppression of gene flow during RI is rarely quantified. Here, we consider a polygenic “magic” trait that is divergently selected across two populations connected by migration, while also serving as the basis of assortative mating, thus generating sexual selection on one or both sexes. We obtain theoretical predictions for divergence at individual trait loci by assuming that the effect of all other loci on any locus can be encapsulated via an effective migration rate, which bears a simple relationship to measurable fitness components of migrants and various early-generation hybrids. Our analysis clarifies how “tipping points” (characterized by an abrupt collapse of adaptive divergence) arise, and when assortative mating can shift the critical level of migration beyond which divergence collapses. We quantify the relative contributions of viability and sexual selection to genome-wide barriers to gene flow and discuss how these depend on existing divergence levels. Our results suggest that effective migration rates provide a useful way of understanding genomic divergence, even in scenarios involving multiple, interacting mechanisms of RI. }, author = {Surendranadh, Parvathy and Sachdeva, Himani}, issn = {1558-5646}, journal = {Evolution}, number = {7}, pages = {1185--1198}, publisher = {Oxford University Press}, title = {{Effect of assortative mating and sexual selection on polygenic barriers to gene flow}}, doi = {10.1093/evolut/qpaf047}, volume = {79}, year = {2025}, } @misc{17344, abstract = {This file contains the Mathematica notebook associated with the paper Effect of assortative mating and sexual selection on polygenic barriers to gene flow. It contains the numerical approximations, analyses, and simulations used in the study. }, author = {Surendranadh, Parvathy and Sachdeva, Himani}, publisher = {Institute of Science and Technology Austria}, title = {{Mathematica notebook for 'Effect of assortative mating and sexual selection on polygenic barriers to gene flow'}}, doi = {10.15479/AT:ISTA:17344}, year = {2024}, } @phdthesis{18515, abstract = {Understanding the role of evolutionary processes in shaping genetic variation has been a primary goal in evolutionary genetics. In this regard, a key question is how genetically distinct populations evolve in the face of gene flow, thereby generating genetic and phenotypic divergence and reproductive isolation (RI). This requires quantifying the role and relative contributions of prezygotic and postzygotic isolating mechanisms on the reduction of gene exchange between populations, and identifying regions in the genome that mediate RI, which is often polygenic. Further, this needs distinguishing neutral and selected regions in the genome, and discerning how selection influences patterns of neutral divergence. Population structure, defined as any deviation from panmixia, such as geographic distribution, movement and mating patterns of individuals, influences how genetic variation is structured in space and shapes the neutral null model. Availability of large scale spatial genomic datasets now enables us to detect signatures of population structure in genetic data and infer population genetic parameters. Such inferences are crucial and have wide applications in biodiversity, conservation genetics, population management and medical genetics. However, inferences are based on assumptions that do not always match the complex reality, thus leading to erroneous conclusions. Moreover, the role and interaction of heterogeneous population density and dispersal, which are ubiquitous in nature, has been challenging to study owing to their mathematical complexity. In such scenarios, feedback between theory, data and simulations can prove to be useful. In this thesis, I examine the effect of population structure on neutral genetic variation and barriers to gene exchange in hybridising populations, thereby bridging together the fields of spatial population genetics and speciation. Despite being a key concept in speciation, reproductive isolation (RI) lacks a quantitative definition and has been used and measured differently across different fields. Chapter 2 gives a quantitative definition of RI, in terms of the effect of genetic differences on gene flow. We give analytical predictions for RI in a range of scenarios, in terms of effective migration rates for discrete populations and barrier strength for continuous populations. In addition to this, we discuss current measures of RI and their limitations, and propose the need for new measures that combine organismal and genetic perspectives of RI. In chapter 3, I examine the combined effect of assortative mating, sexual selection and viability selection on RI. For this, we consider a polygenic ‘magic’ trait under a mainland-island model. We obtain novel theoretical predictions for molecular divergence in terms of effective migration rates, which bears a simple relationship to measurable fitness components of migrants and various early generation hybrids. We explore the conditions under which local adaptation can be maintained despite maladaptive gene flow and quantify the relative contributions of viability and sexual selection to genome-wide barriers to gene flow. The next two chapters of the thesis focus on a hybrid zone of Antirrhinum majus that consist of two subspecies- the magenta flowered A. m. pseudomajus and the yellow flowered A.m. striatum. Previous studies have suggested that flower colour is target of pollinator mediated selection and is influenced only by few genes. While these regions show high genetic differentiation between the subspecies, the rest of the genome is seen to be well mixed. Chapter 4 examines the effects of heterogeneous population density and leptokurtic dispersal on isolation by distance and the distribution of heterozygosity by focusing on non-flower colour markers. Chapter 5 analyses cline shapes and associations among 6 focal flower colour markers to understand how selection and dispersal maintain this hybrid zone. We see sharp coincident stepped clines at all loci and positive associations throughout the hybrid zone, contrary to the expected patterns from diffusive gene flow. With a novel scheme of inferring dispersal combined with multilocus simulations, we show that stepped clines do not reflect genetic barriers to gene flow, but are rather a result of long-distance migration. This framework allows us to get realistic estimates gene flow and selection and shows how traditional cline analysis may lead to inaccurate conclusions when assumptions of the theory are not met. Overall, this thesis investigates how different features of population structure leave detectable signatures in genetic variation, namely in patterns of isolation by distance, linkage disequilibrium and genetic divergence. It also highlights how effective migration rates provide useful way of analysing polygenic architectures and shed new light into hybrid zones. In doing so, I identify scenarios when simple models become insufficient and suggest possibe directions by combining genetic data with simulations.}, author = {Surendranadh, Parvathy}, issn = {2663-337X}, pages = {219}, publisher = {Institute of Science and Technology Austria}, title = {{Effect of population structure on neutral genetic variation and barriers to gene exchange}}, doi = {10.15479/at:ista:18515}, year = {2024}, } @article{12264, abstract = {Reproductive isolation (RI) is a core concept in evolutionary biology. It has been the central focus of speciation research since the modern synthesis and is the basis by which biological species are defined. Despite this, the term is used in seemingly different ways, and attempts to quantify RI have used very different approaches. After showing that the field lacks a clear definition of the term, we attempt to clarify key issues, including what RI is, how it can be quantified in principle, and how it can be measured in practice. Following other definitions with a genetic focus, we propose that RI is a quantitative measure of the effect that genetic differences between populations have on gene flow. Specifically, RI compares the flow of neutral alleles in the presence of these genetic differences to the flow without any such differences. RI is thus greater than zero when genetic differences between populations reduce the flow of neutral alleles between populations. We show how RI can be quantified in a range of scenarios. A key conclusion is that RI depends strongly on circumstances—including the spatial, temporal and genomic context—making it difficult to compare across systems. After reviewing methods for estimating RI from data, we conclude that it is difficult to measure in practice. We discuss our findings in light of the goals of speciation research and encourage the use of methods for estimating RI that integrate organismal and genetic approaches.}, author = {Westram, Anja M and Stankowski, Sean and Surendranadh, Parvathy and Barton, Nicholas H}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, keywords = {Ecology, Evolution, Behavior and Systematics}, number = {9}, pages = {1143--1164}, publisher = {Wiley}, title = {{What is reproductive isolation?}}, doi = {10.1111/jeb.14005}, volume = {35}, year = {2022}, } @article{12265, author = {Westram, Anja M and Stankowski, Sean and Surendranadh, Parvathy and Barton, Nicholas H}, issn = {1420-9101}, journal = {Journal of Evolutionary Biology}, keywords = {Ecology, Evolution, Behavior and Systematics}, number = {9}, pages = {1200--1205}, publisher = {Wiley}, title = {{Reproductive isolation, speciation, and the value of disagreement: A reply to the commentaries on ‘What is reproductive isolation?’}}, doi = {10.1111/jeb.14082}, volume = {35}, 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{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}, } @misc{9192, abstract = {Here are the research data underlying the publication " Effects of fine-scale population structure on inbreeding in a long-term study of snapdragons (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:9192}, year = {2021}, }